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Fixes #2409 Stomach neuroendocrine cells now classified under grouping term #2533

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Fixes #2409 Stomach neuroendocrine cells now classified under grouping term #2533

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f28db90
Update cl-edit.owl
JABelfiore Aug 30, 2024
9742dee
Merge branch 'master' into stomach_ec_cells
JABelfiore Sep 6, 2024
feac4dd
Merge branch 'master' into stomach_ec_cells
JABelfiore Sep 6, 2024
e829c1e
Merge branch 'master' into stomach_ec_cells
JABelfiore Sep 6, 2024
79415ef
G cells, EC cells and D cells under this category
JABelfiore Sep 6, 2024
a83d7a6
Merge branch 'master' into stomach_ec_cells
dosumis Sep 9, 2024
fb024d1
Update cl-edit.owl
dosumis Sep 9, 2024
17276bf
Merge branch 'master' into stomach_ec_cells
dosumis Sep 9, 2024
339c173
Merge branch 'master' into stomach_ec_cells
dosumis Sep 17, 2024
06dd00a
Merge branch 'master' into stomach_ec_cells
Caroline-99 Sep 23, 2024
43f5d05
Merge branch 'master' into stomach_ec_cells
dosumis Sep 25, 2024
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9 changes: 6 additions & 3 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7708,6 +7708,7 @@ 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 @@ -7755,6 +7756,7 @@ 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")
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Type G enteroendocrine cell is not exclusively found in the stomach, it is also found in duodenum and pancreas (https://en.wikipedia.org/wiki/G_cell). It has been inferred that Type G enteroendocrine cell is a subclass of stomach neuroendocrine cell.

To remain consistent with the other patterns, I would suggest keeping Type G enteroendocrine cell as a broad term (e.g. enteroendocrine cell and neuroendocrine cell and gastrin secreting cell and enkephalin secreting cell.

Then create a specific term type G cell of stomach that is type G enteroendocrine cell
and ('part of' some 'epithelium of stomach') or 'part of' some 'mucosa of pyloric antrum'

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))
Expand Down Expand Up @@ -8421,6 +8423,7 @@ 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 @@ -16470,7 +16473,7 @@ 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 @@ -16511,7 +16514,7 @@ 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 @@ -27731,7 +27734,7 @@ 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")
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Please add more information for this term stomach enteroendocrine cell - (ie. references).
Also, the stomach neuroendocrine cell lacks a textual defs, references, synonyms etc.

This could be done in a separate ticket.

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
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