From 97ba1aaa5b89c8b2ff30015290c8496f947e7614 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 11 Feb 2025 12:42:19 +0000 Subject: [PATCH 1/3] def and refs --- src/ontology/cl-edit.owl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ce07a5a69..1722264c7 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3116,6 +3116,7 @@ Declaration(Class(obo:CL_4047034)) Declaration(Class(obo:CL_4047035)) Declaration(Class(obo:CL_4047037)) Declaration(Class(obo:CL_4047040)) +Declaration(Class(obo:CL_4047045)) Declaration(Class(obo:CL_4047051)) Declaration(Class(obo:CL_4047052)) Declaration(Class(obo:CL_4047101)) @@ -25014,7 +25015,7 @@ SubClassOf(obo:CL_0019031 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4047017)) # Class: obo:CL_0019032 (intestinal tuft cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22527717") Annotation(oboInOwl:hasDbXref "PMID:39358509") Annotation(oboInOwl:hasDbXref "PMID:29714721") Annotation(oboInOwl:hasDbXref "PMID:35237268") obo:IAO_0000115 obo:CL_0019032 "A tuft cell that is part of the intestinal epithelium, characterized by a distinctive apical tuft and lateral cytospinules connecting to neighbouring cells. This cell senses luminal stimuli via taste receptors and succinate signalling, initiating type 2 immune responses through the secretion of interleukin-25 while modulating epithelial regeneration through prostaglandin synthesis. It expresses key molecular markers such as doublecortin-like kinase 1 (DCLK1) in mice (Hendel et al., 2022), and KIT proto-oncogene in humans (Huang et al., 2024). Developed from intestinal crypt stem cells, this cell requires transcription factor POU2F3 for its development.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22527717") Annotation(oboInOwl:hasDbXref "PMID:29714721") Annotation(oboInOwl:hasDbXref "PMID:35237268") Annotation(oboInOwl:hasDbXref "PMID:39358509") obo:IAO_0000115 obo:CL_0019032 "A tuft cell that is part of the intestinal epithelium, characterized by a distinctive apical tuft and lateral cytospinules connecting to neighbouring cells. This cell senses luminal stimuli via taste receptors and succinate signalling, initiating type 2 immune responses through the secretion of interleukin-25 while modulating epithelial regeneration through prostaglandin synthesis. It expresses key molecular markers such as doublecortin-like kinase 1 (DCLK1) in mice (Hendel et al., 2022), and KIT proto-oncogene in humans (Huang et al., 2024). Developed from intestinal crypt stem cells, this cell requires transcription factor POU2F3 for its development.") AnnotationAssertion(terms:contributor obo:CL_0019032 ) AnnotationAssertion(terms:date obo:CL_0019032 "2020-10-15T12:47:46Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22527717") oboInOwl:hasExactSynonym obo:CL_0019032 "intestinal brush cell") @@ -33173,6 +33174,15 @@ AnnotationAssertion(rdfs:label obo:CL_4047040 "smooth muscle circular layer cell SubClassOf(obo:CL_4047040 obo:CL_0000192) SubClassOf(obo:CL_4047040 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012368)) +# Class: obo:CL_4047045 (type 3 mucosal glia) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1002/glia.22746") Annotation(oboInOwl:hasDbXref "DOI:10.3389/fimmu.2024.1408744") Annotation(oboInOwl:hasDbXref "DOI:10.3389/fncel.2023.1170309") Annotation(oboInOwl:hasDbXref "PMID:33731961") obo:IAO_0000115 obo:CL_4047045 "An enteric glial cell located in the lamina propria of the intestinal mucosa. This cell typically has four major processes and is positioned in close proximity to the intestinal epithelium. This cell plays important roles in maintaining gut barrier function, regulating intestinal homeostasis, and mediating interactions between the enteric nervous system and the immune system.") +AnnotationAssertion(terms:contributor obo:CL_4047045 ) +AnnotationAssertion(terms:date obo:CL_4047045 "2025-02-11T12:39:11Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4047045 "type 3 mucosal glia") +SubClassOf(obo:CL_4047045 obo:CL_4040002) +SubClassOf(obo:CL_4047045 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000030)) + # Class: obo:CL_4047051 (small intestine BEST4+ enterocyte) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.") From 81c2635a71ee604695a456aec41d98641fa4e243 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 11 Feb 2025 16:59:03 +0000 Subject: [PATCH 2/3] doi to PMID --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 1722264c7..246a0ed3b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -33176,7 +33176,7 @@ SubClassOf(obo:CL_4047040 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_001236 # Class: obo:CL_4047045 (type 3 mucosal glia) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1002/glia.22746") Annotation(oboInOwl:hasDbXref "DOI:10.3389/fimmu.2024.1408744") Annotation(oboInOwl:hasDbXref "DOI:10.3389/fncel.2023.1170309") Annotation(oboInOwl:hasDbXref "PMID:33731961") obo:IAO_0000115 obo:CL_4047045 "An enteric glial cell located in the lamina propria of the intestinal mucosa. This cell typically has four major processes and is positioned in close proximity to the intestinal epithelium. This cell plays important roles in maintaining gut barrier function, regulating intestinal homeostasis, and mediating interactions between the enteric nervous system and the immune system.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33731961") Annotation(oboInOwl:hasDbXref "PMID:25161129") Annotation(oboInOwl:hasDbXref "PMID:37153631") Annotation(oboInOwl:hasDbXref "PMID:38957473") obo:IAO_0000115 obo:CL_4047045 "An enteric glial cell located in the lamina propria of the intestinal mucosa. This cell typically has four major processes and is positioned in close proximity to the intestinal epithelium. This cell plays important roles in maintaining gut barrier function, regulating intestinal homeostasis, and mediating interactions between the enteric nervous system and the immune system.") AnnotationAssertion(terms:contributor obo:CL_4047045 ) AnnotationAssertion(terms:date obo:CL_4047045 "2025-02-11T12:39:11Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4047045 "type 3 mucosal glia") From 43e8b2a061b7bbcc232f85c6d44c2e79e8fbef82 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 18 Feb 2025 11:05:03 +0000 Subject: [PATCH 3/3] second sentence removed --- src/ontology/cl-edit.owl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index d6163b097..7673431d6 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3406,7 +3406,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (preferred_root) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3496,11 +3496,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -33177,7 +33177,7 @@ SubClassOf(obo:CL_4047040 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_001236 # Class: obo:CL_4047043 (type 1 submucosal plexus glia) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.3389/fncel.2023.1170309") Annotation(oboInOwl:hasDbXref "PMID:28487635") Annotation(oboInOwl:hasDbXref "PMID:33731961") obo:IAO_0000115 obo:CL_4047043 "An enteric glial cell that is associated with neuron cell bodies within submucosal ganglia of the gastrointestinal tract. This cell is located in the submucosa, a layer of connective tissue beneath the intestinal mucosa. This cell plays a role in modulating secretomotor neuron activity and contributes to the regulation of digestive fluid secretion and absorption.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.3389/fncel.2023.1170309") Annotation(oboInOwl:hasDbXref "PMID:28487635") Annotation(oboInOwl:hasDbXref "PMID:33731961") obo:IAO_0000115 obo:CL_4047043 "An enteric glial cell that is associated with neuron cell bodies within submucosal ganglia of the gastrointestinal tract. This cell plays a role in modulating secretomotor neuron activity and contributes to the regulation of digestive fluid secretion and absorption.") AnnotationAssertion(terms:contributor obo:CL_4047043 ) AnnotationAssertion(terms:date obo:CL_4047043 "2025-02-10T17:02:28Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33731961") oboInOwl:hasExactSynonym obo:CL_4047043 "type I SMP") @@ -33187,7 +33187,7 @@ SubClassOf(obo:CL_4047043 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000956 # Class: obo:CL_4047045 (type 3 mucosal glia) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33731961") Annotation(oboInOwl:hasDbXref "PMID:25161129") Annotation(oboInOwl:hasDbXref "PMID:37153631") Annotation(oboInOwl:hasDbXref "PMID:38957473") obo:IAO_0000115 obo:CL_4047045 "An enteric glial cell located in the lamina propria of the intestinal mucosa. This cell typically has four major processes and is positioned in close proximity to the intestinal epithelium. This cell plays important roles in maintaining gut barrier function, regulating intestinal homeostasis, and mediating interactions between the enteric nervous system and the immune system.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25161129") Annotation(oboInOwl:hasDbXref "PMID:33731961") Annotation(oboInOwl:hasDbXref "PMID:37153631") Annotation(oboInOwl:hasDbXref "PMID:38957473") obo:IAO_0000115 obo:CL_4047045 "An enteric glial cell located in the lamina propria of the intestinal mucosa. This cell typically has four major processes and is positioned in close proximity to the intestinal epithelium. This cell plays important roles in maintaining gut barrier function, regulating intestinal homeostasis, and mediating interactions between the enteric nervous system and the immune system.") AnnotationAssertion(terms:contributor obo:CL_4047045 ) AnnotationAssertion(terms:date obo:CL_4047045 "2025-02-11T12:39:11Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4047045 "type 3 mucosal glia") @@ -33636,10 +33636,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") Annotation(ob AnnotationAssertion(terms:contributor obo:CL_4052037 ) AnnotationAssertion(terms:date obo:CL_4052037 "2025-02-06T15:03:53Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasExactSynonym obo:CL_4052037 "olfactory tuft cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "tuft-microvillous cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TPRM5+ tuft-MVC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:/10.1101/2022.09.26.509561") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous tuft cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052037 "tuft-microvillous cell") AnnotationAssertion(rdfs:label obo:CL_4052037 "tuft cell of olfactory epithelium") EquivalentClasses(obo:CL_4052037 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001997))) SubClassOf(obo:CL_4052037 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0072091))