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Fixes #2409 Stomach neuroendocrine cells now classified under groupin…
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…g term (#2533)

* Update cl-edit.owl

* G cells, EC cells and D cells under this category

* Update cl-edit.owl

Some more tweaks to fix hierarchy

* type g cell of stomach

Updated definition to reflect location and created new term for type g cell of stomach

* Refs update, logical def amend

* references added, def amended

* removed an axiom

---------

Co-authored-by: David Osumi-Sutherland <[email protected]>
Co-authored-by: CEastwood <[email protected]>
Co-authored-by: Caroline Eastwood <[email protected]>
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@JABelfiore @dosumis @Caroline-99
4 people authored Oct 28, 2024
1 parent 987f2e2 commit 6ef435d
Showing 1 changed file with 15 additions and 5 deletions.
20 changes: 15 additions & 5 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3085,6 +3085,7 @@ Declaration(Class(obo:CL_4047011))
Declaration(Class(obo:CL_4047012))
Declaration(Class(obo:CL_4047018))
Declaration(Class(obo:CL_4047019))
Declaration(Class(obo:CL_4047025))
Declaration(Class(obo:CL_4047051))
Declaration(Class(obo:CL_4047052))
Declaration(Class(obo:CL_4047101))
Expand Down Expand Up @@ -7762,6 +7763,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000502 "FMA:62935")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000502 "D cell")
AnnotationAssertion(rdfs:label obo:CL_0000502 "type D enteroendocrine cell")
SubClassOf(obo:CL_0000502 obo:CL_0000164)
SubClassOf(obo:CL_0000502 obo:CL_0000165)
SubClassOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0070253))

# Class: obo:CL_0000503 (theca cell)
Expand Down Expand Up @@ -7803,15 +7805,15 @@ SubClassOf(obo:CL_0000507 obo:CL_0000167)

# Class: obo:CL_0000508 (type G enteroendocrine cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "MESH:D019863") obo:IAO_0000115 obo:CL_0000508 "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "MESH:D019863") Annotation(oboInOwl:hasDbXref "PMID:10700044") Annotation(oboInOwl:hasDbXref "PMID:35674015") Annotation(oboInOwl:hasDbXref "PMID:37240181") obo:IAO_0000115 obo:CL_0000508 "An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000508 "BTO:0004108")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000508 "FMA:67609")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000508 "G cell")
AnnotationAssertion(rdfs:label obo:CL_0000508 "type G enteroendocrine cell")
SubClassOf(obo:CL_0000508 obo:CL_0000164)
SubClassOf(obo:CL_0000508 obo:CL_0000165)
SubClassOf(obo:CL_0000508 obo:CL_0000506)
SubClassOf(obo:CL_0000508 obo:CL_0000509)
SubClassOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004997))

# Class: obo:CL_0000509 (gastrin secreting cell)

Expand Down Expand Up @@ -8477,6 +8479,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000577 "argentaffin cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000577 "enterochromaffin cell")
AnnotationAssertion(rdfs:label obo:CL_0000577 "type EC enteroendocrine cell")
SubClassOf(obo:CL_0000577 obo:CL_0000164)
SubClassOf(obo:CL_0000577 obo:CL_0000165)
SubClassOf(obo:CL_0000577 obo:CL_0000166)
SubClassOf(obo:CL_0000577 obo:CL_0000458)
SubClassOf(obo:CL_0000577 obo:CL_0000506)
Expand Down Expand Up @@ -16523,7 +16526,7 @@ AnnotationAssertion(terms:contributor obo:CL_0002264 <https://orcid.org/0000-000
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002264 "2010-09-10T10:54:42Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002264 "FMA:83411")
AnnotationAssertion(rdfs:label obo:CL_0002264 "type A cell of stomach")
EquivalentClasses(obo:CL_0002264 ObjectIntersectionOf(obo:CL_0002067 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000945)))
EquivalentClasses(obo:CL_0002264 ObjectIntersectionOf(obo:CL_0002067 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276)))
SubClassOf(obo:CL_0002264 obo:CL_0002067)

# Class: obo:CL_0002265 (type D cell of colon)
Expand Down Expand Up @@ -16564,7 +16567,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002267 "delta cell of stoma
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002267 "stomach D-cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002267 "stomach delta cell")
AnnotationAssertion(rdfs:label obo:CL_0002267 "type D cell of stomach")
EquivalentClasses(obo:CL_0002267 ObjectIntersectionOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000945)))
EquivalentClasses(obo:CL_0002267 ObjectIntersectionOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276)))
SubClassOf(obo:CL_0002267 obo:CL_0000502)
SubClassOf(obo:CL_0002267 obo:CL_0002659)

Expand Down Expand Up @@ -27789,7 +27792,7 @@ EquivalentClasses(obo:CL_1001516 ObjectIntersectionOf(obo:CL_0000164 ObjectSomeV

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MP:0010803") obo:IAO_0000115 obo:CL_1001517 "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach.")
AnnotationAssertion(rdfs:label obo:CL_1001517 "stomach enteroendocrine cell")
EquivalentClasses(obo:CL_1001517 ObjectIntersectionOf(obo:CL_0000164 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001160)))
EquivalentClasses(obo:CL_1001517 ObjectIntersectionOf(obo:CL_0000164 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000945)))

# Class: obo:CL_1001561 (vomeronasal sensory neuron)

Expand Down Expand Up @@ -32686,6 +32689,13 @@ AnnotationAssertion(terms:date obo:CL_4047019 "2024-09-24T12:11:09Z"^^xsd:dateTi
AnnotationAssertion(rdfs:label obo:CL_4047019 "early enterocyte"@en)
EquivalentClasses(obo:CL_4047019 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0013740)))

# Class: obo:CL_4047025 (type G cell of stomach)

AnnotationAssertion(terms:contributor obo:CL_4047025 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_4047025 "2024-10-24T10:43:22Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4047025 "type G cell of stomach"@en)
EquivalentClasses(obo:CL_4047025 ObjectIntersectionOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276)))

# 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.")
Expand Down

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