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Merge branch 'master' into 2843-ntr-stomach-smooth-muscle-circular-la…
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…yer-cell
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@JABelfiore
JABelfiore authored Jan 31, 2025
2 parents 184d0a5 + 850c710 commit 0f74961
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24 changes: 12 additions & 12 deletions src/mappings/fbbt.sssom.tsv
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#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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76 changes: 74 additions & 2 deletions src/ontology/cl-edit.owl
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Expand Up @@ -3049,6 +3049,8 @@ Declaration(Class(obo:CL_4033091))
Declaration(Class(obo:CL_4033092))
Declaration(Class(obo:CL_4033093))
Declaration(Class(obo:CL_4033094))
Declaration(Class(obo:CL_4033095))
Declaration(Class(obo:CL_4033096))
Declaration(Class(obo:CL_4040000))
Declaration(Class(obo:CL_4040001))
Declaration(Class(obo:CL_4040002))
Expand Down Expand Up @@ -3147,6 +3149,10 @@ Declaration(Class(obo:CL_4052029))
Declaration(Class(obo:CL_4052030))
Declaration(Class(obo:CL_4052031))
Declaration(Class(obo:CL_4052032))
Declaration(Class(obo:CL_4052033))
Declaration(Class(obo:CL_4052034))
Declaration(Class(obo:CL_4052035))
Declaration(Class(obo:CL_4052036))
Declaration(Class(obo:CL_4052048))
Declaration(Class(obo:CL_4052049))
Declaration(Class(obo:CP_0000000))
Expand All @@ -3160,6 +3166,7 @@ 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 @@ -9510,7 +9517,7 @@ AnnotationAssertion(rdfs:label obo:CL_0000682 "M cell of gut")
SubClassOf(obo:CL_0000682 obo:CL_0000066)
SubClassOf(obo:CL_0000682 obo:CL_0000473)
SubClassOf(obo:CL_0000682 obo:CL_0000627)
SubClassOf(obo:CL_0000682 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003929))
SubClassOf(obo:CL_0000682 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693))

# Class: obo:CL_0000683 (ependymoglial cell)

Expand Down Expand Up @@ -25161,9 +25168,11 @@ EquivalentClasses(obo:CL_1000272 ObjectIntersectionOf(obo:CL_0000151 ObjectSomeV

# Class: obo:CL_1000274 (trophectodermal cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22918806") obo:IAO_0000115 obo:CL_1000274 "An extraembryonic cell that is part of the trophectoderm, representing the first lineage to differentiate in the embryo. This cell is crucial for implantation into the uterine wall and differentiates into trophoblast cells, which contribute to placenta formation and facilitate maternal-fetal nutrient and signal exchange.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_1000274 "trophectoderm cell")
AnnotationAssertion(rdfs:label obo:CL_1000274 "trophectodermal cell")
SubClassOf(obo:CL_1000274 obo:CL_0000349)
EquivalentClasses(obo:CL_1000274 ObjectIntersectionOf(obo:CL_0000349 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004345)))
SubClassOf(obo:CL_1000274 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000351))

# Class: obo:CL_1000275 (smooth muscle cell of small intestine)

Expand Down Expand Up @@ -32429,6 +32438,26 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35798993") Annotation(ob
AnnotationAssertion(rdfs:label obo:CL_4033094 "age-associated B cell")
SubClassOf(obo:CL_4033094 obo:CL_0000787)

# Class: obo:CL_4033095 (diffuse bipolar 4a cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31995762") Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.11.07.566105") obo:IAO_0000115 obo:CL_4033095 "An ON bipolar cell that has high expression of DIRC3, KCNJ3, LINC01915, PTPRK compared with other bipolar cells.")
AnnotationAssertion(terms:contributor obo:CL_4033095 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033095 "2025-01-14T13:48:42Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.11.07.566105") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033095 "DB4a")
AnnotationAssertion(rdfs:label obo:CL_4033095 "diffuse bipolar 4a cell")
SubClassOf(obo:CL_4033095 obo:CL_0000749)
SubClassOf(obo:CL_4033095 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_9606))

# Class: obo:CL_4033096 (diffuse bipolar 4b cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31995762") Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.11.07.566105") obo:IAO_0000115 obo:CL_4033096 "An ON bipolar cell that has high expression of NOS1AP compared with other bipolar cells.")
AnnotationAssertion(terms:contributor obo:CL_4033096 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:date obo:CL_4033096 "2025-01-14T13:49:08Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.11.07.566105") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033096 "DB4b")
AnnotationAssertion(rdfs:label obo:CL_4033096 "diffuse bipolar 4b cell")
SubClassOf(obo:CL_4033096 obo:CL_0000749)
SubClassOf(obo:CL_4033096 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_9606))

# Class: obo:CL_4040000 (glial restricted tripotential precursor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10719353") obo:IAO_0000115 obo:CL_4040000 "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes.")
Expand Down Expand Up @@ -33283,6 +33312,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") Annotation(obo
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasRelatedSynonym obo:CL_4052011 "follicular enterocyte")
AnnotationAssertion(rdfs:label obo:CL_4052011 "follicle associated enterocyte")
SubClassOf(obo:CL_4052011 obo:CL_0000584)
SubClassOf(obo:CL_4052011 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693))

# Class: obo:CL_4052012 (interna theca cell)

Expand Down Expand Up @@ -33514,6 +33544,48 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") rdfs:comment
AnnotationAssertion(rdfs:label obo:CL_4052032 "granzyme H-associated CD8 T cell")
EquivalentClasses(obo:CL_4052032 ObjectIntersectionOf(obo:CL_0000909 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000003490)))

# Class: obo:CL_4052033 (biliary tuft cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35245089") Annotation(oboInOwl:hasDbXref "PMID:37863104") obo:IAO_0000115 obo:CL_4052033 "A tuft cell that is part of the extrahepatic biliary tree, including the gallbladder and extrahepatic bile ducts. It shares a core genetic program with intestinal tuft cells but has unique tissue-specific genes. Biliary tuft cell functions as a bile acid-sensitive regulator, suppressing inflammation and modulating microbiome-dependent neutrophil infiltration in biliary tissues. Unlike its intestinal counterparts, this cell decreases in number postnatally as bile acid production matures, with its abundance negatively regulated by bile acids.")
AnnotationAssertion(terms:contributor obo:CL_4052033 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052033 "2025-01-20T14:39:06Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35245089") oboInOwl:hasExactSynonym obo:CL_4052033 "gallbladder/extrahepatic bile duct tuft cell")
AnnotationAssertion(rdfs:label obo:CL_4052033 "biliary tuft cell")
SubClassOf(obo:CL_4052033 obo:CL_0002204)
SubClassOf(obo:CL_4052033 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050728))

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

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:35668088") Annotation(oboInOwl:hasDbXref "PMID:36351364") Annotation(oboInOwl:hasDbXref "PMID:36961668") 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_4052035 (tuft cell of pancreatic duct)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30904566") Annotation(oboInOwl:hasDbXref "PMID:32717220") obo:IAO_0000115 obo:CL_4052035 "A tuft cell that is part of the epithelium of pancreatic duct. Present in humans and rats, this cell is absent in the murine pancreas under normal conditions but emerges during acinar-to-ductal metaplasia triggered by injury, inflammation, or oncogenic mutations. It modulates the immune response and protects against pancreatic ductal adenocarcinoma progression by producing suppressive eicosanoids, such as prostaglandin D2. A tuft cell in the pancreatic duct highly expresses the transcription factor POU2F3, which is essential for its development and presence.")
AnnotationAssertion(terms:contributor obo:CL_4052035 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052035 "2025-01-16T11:50:08Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9749964") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic brush cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32717220") oboInOwl:hasExactSynonym obo:CL_4052035 "pancreatic tuft cell")
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_4052036 (tuft cell of nasal cavity)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30379593") Annotation(oboInOwl:hasDbXref "PMID:38306414") obo:IAO_0000115 obo:CL_4052036 "A tuft cell that is part of the nasal cavity epithelium, located in both the respiratory and olfactory epithelia of the nose. This cell plays key roles in chemosensation, lipid mediator production, immune responses, and epithelial homeostasis.")
AnnotationAssertion(terms:contributor obo:CL_4052036 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052036 "2025-01-21T09:04:03Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34692913") oboInOwl:hasExactSynonym obo:CL_4052036 "nasal brush cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasExactSynonym obo:CL_4052036 "nasal tuft cell")
AnnotationAssertion(rdfs:label obo:CL_4052036 "tuft cell of nasal cavity")
EquivalentClasses(obo:CL_4052036 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005384)))

# 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>))
Expand Down
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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