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Merge branch 'master' into 2887-ntrtype-1-submucosal-plexus-glia
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@Caroline-99
Caroline-99 committed Feb 11, 2025
2 parents 2b675d3 + 27648ff commit 72d6583
Showing 1 changed file with 41 additions and 16 deletions.
57 changes: 41 additions & 16 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3156,6 +3156,8 @@ Declaration(Class(obo:CL_4052033))
Declaration(Class(obo:CL_4052034))
Declaration(Class(obo:CL_4052035))
Declaration(Class(obo:CL_4052036))
Declaration(Class(obo:CL_4052037))
Declaration(Class(obo:CL_4052038))
Declaration(Class(obo:CL_4052048))
Declaration(Class(obo:CL_4052049))
Declaration(Class(obo:CP_0000000))
Expand Down Expand Up @@ -3403,7 +3405,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition")

AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to")

# Annotation Property: obo:IAO_0000700 (preferred_root)
# Annotation Property: obo:IAO_0000700 (has ontology root term)

AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root")

Expand Down Expand Up @@ -3493,11 +3495,11 @@ 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")

Expand Down Expand Up @@ -15568,9 +15570,10 @@ AnnotationAssertion(terms:contributor obo:CL_0002167 <https://orcid.org/0000-000
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002167 "2010-08-26T01:47:13Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002167 "FMA:67870")
AnnotationAssertion(rdfs:label obo:CL_0002167 "olfactory epithelial cell")
EquivalentClasses(obo:CL_0002167 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050911)))
EquivalentClasses(obo:CL_0002167 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001997)))
SubClassOf(obo:CL_0002167 obo:CL_0000098)
SubClassOf(obo:CL_0002167 obo:CL_0000710)
SubClassOf(obo:CL_0002167 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050911))

# Class: obo:CL_0002168 (border cell of cochlea)

Expand All @@ -15589,7 +15592,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002169 "2010-08-26T01:58:54Z"
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0002169 "horizontal basal cell")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002169 "FMA:62303")
AnnotationAssertion(rdfs:label obo:CL_0002169 "basal cell of olfactory epithelium")
EquivalentClasses(obo:CL_0002169 ObjectIntersectionOf(obo:CL_0002167 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001997)))
EquivalentClasses(obo:CL_0002169 ObjectIntersectionOf(obo:CL_0002167 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000482)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002169 obo:CL_0002167)

# Class: obo:CL_0002170 (keratinized cell of the oral mucosa)
Expand Down Expand Up @@ -15940,21 +15943,18 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002202 "FMA:66816")
AnnotationAssertion(rdfs:label obo:CL_0002202 "epithelial cell of tracheobronchial tree")
EquivalentClasses(obo:CL_0002202 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008397)))

# Class: obo:CL_0002203 (brush cell of epithelium proper of large intestine)
# Class: obo:CL_0002203 (tuft cell of large intestine)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_0002203 "Brush cell found in the epithelial layer of the colon.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:35271673") obo:IAO_0000115 obo:CL_0002203 "A tuft cell that is part of the epithelium of large intestine.")
AnnotationAssertion(terms:contributor obo:CL_0002203 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002203 "2010-09-02T02:20:50Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002203 "FMA:263222")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002203 "brush cell of epithelium proper of large intestine")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865") oboInOwl:hasExactSynonym obo:CL_0002203 "brush cell of large intestine")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865") oboInOwl:hasExactSynonym obo:CL_0002203 "tuft cell of epithelium of large intestine")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865") oboInOwl:hasExactSynonym obo:CL_0002203 "tuft cell of large intestine")
AnnotationAssertion(rdfs:comment obo:CL_0002203 "Brush cells are a distinct cell type from brush border cell-types.")
AnnotationAssertion(rdfs:label obo:CL_0002203 "brush cell of epithelium proper of large intestine")
EquivalentClasses(obo:CL_0002203 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000059)))
SubClassOf(obo:CL_0002203 obo:CL_0002204)
SubClassOf(obo:CL_0002203 obo:CL_0002253)
SubClassOf(obo:CL_0002203 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001278))
AnnotationAssertion(rdfs:label obo:CL_0002203 "tuft cell of large intestine")
EquivalentClasses(obo:CL_0002203 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001278)))

# Class: obo:CL_0002204 (brush cell)

Expand Down Expand Up @@ -29150,12 +29150,12 @@ EquivalentClasses(obo:CL_2000083 ObjectIntersectionOf(obo:CL_0000346 ObjectSomeV

# Class: obo:CL_2000084 (conjunctiva goblet cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") obo:IAO_0000115 obo:CL_2000084 "Any goblet cell that is part of a conjunctiva.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:27091323") Annotation(oboInOwl:hasDbXref "PMID:28475124") Annotation(oboInOwl:hasDbXref "PMID:31734511") obo:IAO_0000115 obo:CL_2000084 "A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (containing MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation.")
AnnotationAssertion(terms:contributor obo:CL_2000084 <http://www.wikidata.org/entity/Q35563349>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_2000084 "2014-12-02T19:28:38Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:id obo:CL_2000084 "CL:2000084")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31734511") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_2000084 "CGC")
AnnotationAssertion(rdfs:label obo:CL_2000084 "conjunctiva goblet cell")
EquivalentClasses(obo:CL_2000084 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001811)))
EquivalentClasses(obo:CL_2000084 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006763)))

# Class: obo:CL_2000085 (mononuclear cell of umbilical cord)

Expand Down Expand Up @@ -33620,6 +33620,31 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasE
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_4052037 (tuft cell of olfactory epithelium)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") Annotation(oboInOwl:hasDbXref "doi:/10.1101/2022.09.26.509561") obo:IAO_0000115 obo:CL_4052037 "A tuft cell that is part of the olfactory epithelium, characterized by a globular body and the expression of neurogranin (Nrgn) in mice. This cell plays a crucial role in allergen recognition and regulating olfactory stem cell proliferation via TRPM5-dependent ATP sensing and cysteinyl leukotriene production. Unlike nasal respiratory tuft cells, it has low to absent expression of taste receptors, including the G protein Gα gustducin, and rarely contacts olfactory sensory neurons directly.")
AnnotationAssertion(terms:contributor obo:CL_4052037 <https://orcid.org/0009-0000-8480-9277>)
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 "doi:/10.1101/2022.09.26.509561") oboInOwl:hasRelatedSynonym obo:CL_4052037 "TRPM5+ microvillous tuft 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))

# Class: obo:CL_4052038 (tuft cell of nasal cavity respiratory epithelium)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30379593") Annotation(oboInOwl:hasDbXref "PMID:34932383") Annotation(oboInOwl:hasDbXref "PMID:38306414") obo:IAO_0000115 obo:CL_4052038 "A tuft cell that is part of the nasal cavity respiratory epithelium. Acting as a chemosensor, it detects bitter taste ligands and bacterial signals via taste receptors, maintaining epithelial-microbial homeostasis by stimulating antimicrobial peptide secretion from adjacent epithelial cells. This cell is a major source of IL-25, promoting type 2 immune responses and potentially contributing to chronic rhinosinusitis (O'Leary et al., 2019).")
AnnotationAssertion(terms:contributor obo:CL_4052038 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052038 "2025-02-06T15:28:14Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052038 "Gɑ-gustducin high respiratory tuft cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052038 "nasal respiratory solitary chemosensory cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38306414") oboInOwl:hasRelatedSynonym obo:CL_4052038 "tuft-solitary chemosensory cell")
AnnotationAssertion(rdfs:label obo:CL_4052038 "tuft cell of nasal cavity respiratory epithelium")
EquivalentClasses(obo:CL_4052038 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005385)))

# 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.")
Expand Down

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