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Fixes #2909 NTR- tuft cell of thymus (#2912)
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* Fixes #2909 NTR- tuft cell of thymus

- Added a new term with textual and logical defs, synonyms and references
-NOTE - GO term cytospinule will be linked to this term once available on GO

* Update cl-edit.owl

* Updated definition and added a link to GO
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@Caroline-99
Caroline-99 authored Jan 17, 2025
1 parent d6c9002 commit e26881d
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Showing 8 changed files with 1,407 additions and 1,073 deletions.
24 changes: 12 additions & 12 deletions src/mappings/fbbt.sssom.tsv
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@@ -1,17 +1,17 @@
#curie_map:
# CL: http://purl.obolibrary.org/obo/CL_
# FBbt: http://purl.obolibrary.org/obo/FBbt_
# ORCID: https://orcid.org/
# obo: http://purl.obolibrary.org/obo/
#mapping_set_id: http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv
#mapping_set_description: Mappings between the Drosophila Anatomy Ontology and foreign ontologies.
# CL: "http://purl.obolibrary.org/obo/CL_"
# FBbt: "http://purl.obolibrary.org/obo/FBbt_"
# ORCID: "https://orcid.org/"
# obo: "http://purl.obolibrary.org/obo/"
#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
#creator_id:
# - ORCID:0000-0002-1373-1705
# - ORCID:0000-0002-6095-8718
#license: https://creativecommons.org/licenses/by/4.0/
#subject_source: obo:fbbt.owl
#object_source: obo:cl.owl
#mapping_date: 2024-07-12
# - "ORCID:0000-0002-1373-1705"
# - "ORCID:0000-0002-6095-8718"
#license: "https://creativecommons.org/licenses/by/4.0/"
#subject_source: "obo:fbbt.owl"
#object_source: "obo:cl.owl"
#mapping_date: "2024-07-12"
subject_id subject_label predicate_id object_id object_label mapping_justification
FBbt:00000092 primordial germ cell semapv:crossSpeciesExactMatch CL:0000301 pole cell semapv:ManualMappingCuration
FBbt:00000124 epithelial cell semapv:crossSpeciesExactMatch CL:0000066 epithelial cell semapv:ManualMappingCuration
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12 changes: 6 additions & 6 deletions src/mappings/zfa.sssom.tsv
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@@ -1,10 +1,10 @@
#curie_map:
# CL: http://purl.obolibrary.org/obo/CL_
# ZFA: http://purl.obolibrary.org/obo/ZFA_
#mapping_set_id: http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv
#license: https://creativecommons.org/licenses/by/3.0/
#subject_source: http://purl.obolibrary.org/obo/zfa.owl
#object_source: http://purl.obolibrary.org/obo/cl.owl
# CL: "http://purl.obolibrary.org/obo/CL_"
# ZFA: "http://purl.obolibrary.org/obo/ZFA_"
#mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv"
#license: "https://creativecommons.org/licenses/by/3.0/"
#subject_source: "http://purl.obolibrary.org/obo/zfa.owl"
#object_source: "http://purl.obolibrary.org/obo/cl.owl"
subject_id subject_label predicate_id object_id object_label mapping_justification
ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 adaxial cell semapv:UnspecifiedMatching
ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 yolk cell semapv:UnspecifiedMatching
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14 changes: 14 additions & 0 deletions src/ontology/cl-edit.owl
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Expand Up @@ -3149,6 +3149,7 @@ Declaration(Class(obo:CL_4052030))
Declaration(Class(obo:CL_4052031))
Declaration(Class(obo:CL_4052032))
Declaration(Class(obo:CL_4052035))
Declaration(Class(obo:CL_4052034))
Declaration(Class(obo:CL_4052048))
Declaration(Class(obo:CL_4052049))
Declaration(Class(obo:CP_0000000))
Expand All @@ -3162,6 +3163,7 @@ Declaration(Class(obo:CP_0000040))
Declaration(Class(obo:CP_0000043))
Declaration(Class(obo:D96882F1-8709-49AB-BCA9-772A67EA6C33))
Declaration(Class(obo:GO_0001552))
Declaration(Class(obo:GO_0002491))
Declaration(Class(obo:GO_0005903))
Declaration(Class(obo:GO_0005927))
Declaration(Class(obo:GO_0019626))
Expand Down Expand Up @@ -33537,6 +33539,18 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32717220") oboInOwl:hasE
AnnotationAssertion(rdfs:label obo:CL_4052035 "tuft cell of pancreatic duct")
EquivalentClasses(obo:CL_4052035 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0009970)))

# Class: obo:CL_4052034 (tuft cell of thymus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:36961668") Annotation(oboInOwl:hasDbXref "PMID:35668088") Annotation(oboInOwl:hasDbXref "PMID:36351364") obo:IAO_0000115 obo:CL_4052034 "A tuft cell that is part of the medullary epithelium of the thymus, characterized by lateral microvilli and specific markers, including L1CAM in both mice (Zhang et al., 2022) and humans (Sun et al., 2023), as well as MHC II in mice (Kotas et al., 2023). This cell is pivotal in immune functions such as antigen presentation, central tolerance, and type 2 immunity. A tuft cell in the thymus exhibits characteristics of both a medullary thymic epithelial cell (mTEC) and a peripheral tuft cell. Its development is governed by transcription factors such as POU2F3.")
AnnotationAssertion(terms:contributor obo:CL_4052034 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052034 "2025-01-16T11:29:54Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") oboInOwl:hasExactSynonym obo:CL_4052034 "thymic tuft cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") rdfs:comment obo:CL_4052034 "A thymic tuft cell is a subset of terminally differentiated medullary thymic epithelial cell comprising 5-10% of total mTECs. Lineage-tracing studies indicate that this cell arises from mature MHCII mTECs, with development occurring through both Aire-dependent and Aire-independent pathways. However, its exact origins remain unclear.")
AnnotationAssertion(rdfs:label obo:CL_4052034 "tuft cell of thymus")
EquivalentClasses(obo:CL_4052034 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003846)))
SubClassOf(obo:CL_4052034 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002124))
SubClassOf(obo:CL_4052034 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002491))

# Class: obo:CL_4052048 (intercalated cell of salivary gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.")
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4 changes: 2 additions & 2 deletions src/ontology/components/cellxgene_subset.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/cl/components/cellxgene_subset.owl>
<http://purl.obolibrary.org/obo/cl/releases/2025-01-07/components/cellxgene_subset.owl>
Annotation(owl:versionInfo "2025-01-07")
<http://purl.obolibrary.org/obo/cl/releases/2025-01-17/components/cellxgene_subset.owl>
Annotation(owl:versionInfo "2025-01-17")

Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000001>))
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3 changes: 2 additions & 1 deletion src/ontology/imports/go_terms.txt
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Expand Up @@ -18,4 +18,5 @@ GO:0050893
GO:0001552
GO:0019626
GO:0098535
GO:0046697
GO:0046697
GO:0002491
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