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

JABelfiore · 2024-08-30T15:55:17Z

Stomach neuroendocrine cells now classified under grouping term

dosumis · 2024-09-09T09:33:38Z

#gogoeditdiff

github-actions · 2024-09-09T09:38:44Z

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-10-28/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-10-28/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

stomach neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000222`

Removed

stomach neuroendocrine cell definition "A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles."
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell has_broad_synonym "diffuse endocrine system cell"
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell has_broad_synonym "DES cell"
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell SubClassOf epithelial cell of stomach
stomach neuroendocrine cell SubClassOf enteroendocrine cell

Added

stomach neuroendocrine cell definition "Any neuroendocrine cell that is part of some stomach."
- database_cross_reference "FBC:Autogenerated"
stomach neuroendocrine cell SubClassOf stomach enteroendocrine cell

type A cell of stomach `http://purl.obolibrary.org/obo/CL_0002264`

Removed

type A cell of stomach SubClassOf epithelial cell of stomach

Added

type A cell of stomach SubClassOf stomach enteroendocrine cell

type D cell of stomach `http://purl.obolibrary.org/obo/CL_0002267`

Added

type D cell of stomach SubClassOf stomach neuroendocrine cell

type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502`

Added

type D enteroendocrine cell SubClassOf neuroendocrine cell

type G cell of stomach `http://purl.obolibrary.org/obo/CL_4047025`

Added

type G cell of stomach definition "."
- database_cross_reference "FBC:Autogenerated"
type G cell of stomach date "2024-10-24T10:43:22Z"^^dateTime
type G cell of stomach label "type G cell of stomach"@en
type G cell of stomach contributor 0009-0005-7919-4905
Class: type G cell of stomach
type G cell of stomach SubClassOf type G enteroendocrine cell

type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508`

Removed

type G enteroendocrine cell definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "ISBN:0517223651"
- database_cross_reference "MESH:D019863"
type G enteroendocrine cell SubClassOf epithelial cell of stomach

Added

type G enteroendocrine cell definition "An endocrine cell found in the stomach, duodenum and pancreas 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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "ISBN:0517223651"
- database_cross_reference "MESH:D019863"
type G enteroendocrine cell SubClassOf neuroendocrine cell

github-actions · 2024-09-09T09:38:46Z

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

stomach enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001517`

Removed

stomach enteroendocrine cell EquivalentTo enteroendocrine cell and (part of some fundus of stomach)

Added

stomach enteroendocrine cell EquivalentTo enteroendocrine cell and (part of some stomach)

stomach neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000222`

Removed

stomach neuroendocrine cell definition "A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles."
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell has_broad_synonym "diffuse endocrine system cell"
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell has_broad_synonym "DES cell"
- database_cross_reference "PMID:15153415"
stomach neuroendocrine cell SubClassOf capable of some acid secretion

type A cell of stomach `http://purl.obolibrary.org/obo/CL_0002264`

Removed

type A cell of stomach EquivalentTo type A enteroendocrine cell and (part of some stomach)

Added

type A cell of stomach EquivalentTo type A enteroendocrine cell and (part of some epithelium of stomach)

type D cell of stomach `http://purl.obolibrary.org/obo/CL_0002267`

Removed

type D cell of stomach EquivalentTo type D enteroendocrine cell and (part of some stomach)

Added

type D cell of stomach EquivalentTo type D enteroendocrine cell and (part of some epithelium of stomach)

type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502`

Added

type D enteroendocrine cell SubClassOf neuroendocrine cell

type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577`

Added

type EC enteroendocrine cell SubClassOf neuroendocrine cell

type G cell of stomach `http://purl.obolibrary.org/obo/CL_4047025`

Added

type G cell of stomach date "2024-10-24T10:43:22Z"^^dateTime
type G cell of stomach label "type G cell of stomach"@en
type G cell of stomach contributor 0009-0005-7919-4905
Class: type G cell of stomach
type G cell of stomach EquivalentTo (type G enteroendocrine cell and (part of some epithelium of stomach)) or (part of some mucosa of pyloric antrum)
type G cell of stomach SubClassOf type G enteroendocrine cell

type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508`

Removed

type G enteroendocrine cell definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "ISBN:0517223651"
- database_cross_reference "MESH:D019863"
type G enteroendocrine cell SubClassOf part of some mucosa of pyloric antrum

Added

type G enteroendocrine cell definition "An endocrine cell found in the stomach, duodenum and pancreas 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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "ISBN:0517223651"
- database_cross_reference "MESH:D019863"
type G enteroendocrine cell SubClassOf neuroendocrine cell

Some more tweaks to fix hierarchy

dosumis · 2024-09-17T13:18:00Z

#gogoeditdiff

Caroline-99 · 2024-09-24T11:06:10Z

src/ontology/cl-edit.owl

@@ -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")


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'

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

src/ontology/cl-edit.owl

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

Caroline-99 · 2024-10-24T11:33:10Z

#gogoeditdiff

Caroline-99 · 2024-10-24T14:04:55Z

src/ontology/cl-edit.owl

+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 ObjectUnionOf(ObjectIntersectionOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276)) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004997)))
+SubClassOf(obo:CL_4047025 obo:CL_0000508)


No need to add SubclassOf type G enteroendocrine cell . This is inferred.

Removed on account of inference

Caroline-99 · 2024-10-24T14:06:04Z

src/ontology/cl-edit.owl

+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 ObjectUnionOf(ObjectIntersectionOf(obo:CL_0000508 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001276)) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004997)))


This logical definition is not correct - I believe we can't use part of this OR part of this

('type G enteroendocrine cell' and ('part of' some 'epithelium of stomach')) or ('part of' some 'mucosa of pyloric antrum').

In my previous comment, I meant you can use

('type G enteroendocrine cell' and ('part of' some 'epithelium of stomach'))

OR

('type G enteroendocrine cell' and ('part of' some 'mucosa of pyloric antrum')).

Depends on how specific you want it to be. Sorry should have been clearer.

Looking more into literature, It seems to me thatpart of some pyloric gland- which is a synonym for pyloric antrum glands might be more suitable but it is up to you. Epithelium of stomach would also work.

I found this

(G cells are found deep within the pyloric glands of the stomach antrum.) https://en.wikipedia.org/wiki/G_cell

Amended to first option only

Caroline-99 · 2024-10-24T14:17:00Z

src/ontology/cl-edit.owl

@@ -7798,15 +7800,15 @@ 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") obo:IAO_0000115 obo:CL_0000508 "An endocrine cell found in the stomach, duodenum and pancreas 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.")


can you please add references to support the new textual defs? I remember when we discussed it in the meeting, there weren't enough evidence to show that this cell is in the pancreas but we found few references showing their presence in the stomach and duodenum.

new defs added

Caroline-99 · 2024-10-28T14:21:14Z

#gogoeditdiff

Update cl-edit.owl

f28db90

JABelfiore changed the title ~~Stomach neuroendocrine cells now classified under grouping term~~ Fixes #2409 Stomach neuroendocrine cells now classified under grouping term Sep 6, 2024

JABelfiore linked an issue Sep 6, 2024 that may be closed by this pull request

Stomach neuroendocrine cells not all classified under grouping term #2409

Closed

JABelfiore and others added 4 commits September 6, 2024 10:21

Merge branch 'master' into stomach_ec_cells

9742dee

Merge branch 'master' into stomach_ec_cells

feac4dd

Merge branch 'master' into stomach_ec_cells

e829c1e

G cells, EC cells and D cells under this category

79415ef

JABelfiore self-assigned this Sep 6, 2024

JABelfiore requested a review from Caroline-99 September 6, 2024 15:22

Merge branch 'master' into stomach_ec_cells

a83d7a6

dosumis added 3 commits September 9, 2024 13:04

Update cl-edit.owl

fb024d1

Some more tweaks to fix hierarchy

Merge branch 'master' into stomach_ec_cells

17276bf

Merge branch 'master' into stomach_ec_cells

339c173

Merge branch 'master' into stomach_ec_cells

06dd00a

Caroline-99 requested changes Sep 24, 2024

View reviewed changes

dosumis added 2 commits September 25, 2024 20:10

Merge branch 'master' into stomach_ec_cells

43f5d05

Merge branch 'master' into stomach_ec_cells

9a14e72

dosumis added this to the Milestone finishing - 14/10/24 milestone Oct 9, 2024

JABelfiore and others added 3 commits October 24, 2024 11:51

Merge branch 'master' into stomach_ec_cells

c14f051

type g cell of stomach

c964fe2

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

Merge branch 'master' into stomach_ec_cells

ca2f783

Caroline-99 requested changes Oct 24, 2024

View reviewed changes

JABelfiore and others added 2 commits October 28, 2024 13:52

Refs update, logical def amend

70f3d4d

Merge branch 'master' into stomach_ec_cells

d72778b

JABelfiore requested a review from Caroline-99 October 28, 2024 13:53

Merge branch 'master' into stomach_ec_cells

e925982

Caroline-99 and others added 5 commits October 28, 2024 14:25

Merge branch 'master' into stomach_ec_cells

0b5a5eb

references added, def amended

91d3393

Merge branch 'master' into stomach_ec_cells

cab03d6

removed an axiom

55f672c

Merge branch 'master' into stomach_ec_cells

3b5d091

Caroline-99 approved these changes Oct 28, 2024

View reviewed changes

JABelfiore merged commit 6ef435d into master Oct 28, 2024
1 check passed

JABelfiore deleted the stomach_ec_cells branch October 28, 2024 15:47

		@@ -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")

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

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

Conversation

JABelfiore commented Aug 30, 2024

dosumis commented Sep 9, 2024

github-actions bot commented Sep 9, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

stomach neuroendocrine cell http://purl.obolibrary.org/obo/CL_1000222

Removed

Added

type A cell of stomach http://purl.obolibrary.org/obo/CL_0002264

Removed

Added

type D cell of stomach http://purl.obolibrary.org/obo/CL_0002267

Added

type D enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000502

Added

type G cell of stomach http://purl.obolibrary.org/obo/CL_4047025

Added

type G enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000508

Removed

Added

github-actions bot commented Sep 9, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

stomach enteroendocrine cell http://purl.obolibrary.org/obo/CL_1001517

Removed

Added

stomach neuroendocrine cell http://purl.obolibrary.org/obo/CL_1000222

Removed

type A cell of stomach http://purl.obolibrary.org/obo/CL_0002264

Removed

Added

type D cell of stomach http://purl.obolibrary.org/obo/CL_0002267

Removed

Added

type D enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000502

Added

type EC enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000577

Added

type G cell of stomach http://purl.obolibrary.org/obo/CL_4047025

Added

type G enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000508

Removed

Added

dosumis commented Sep 17, 2024

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stomach neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000222`

type A cell of stomach `http://purl.obolibrary.org/obo/CL_0002264`

type D cell of stomach `http://purl.obolibrary.org/obo/CL_0002267`

type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502`

type G cell of stomach `http://purl.obolibrary.org/obo/CL_4047025`

type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508`

github-actions bot commented Sep 9, 2024 •

edited

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stomach enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001517`

stomach neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000222`

type A cell of stomach `http://purl.obolibrary.org/obo/CL_0002264`

type D cell of stomach `http://purl.obolibrary.org/obo/CL_0002267`

type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502`

type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577`

type G cell of stomach `http://purl.obolibrary.org/obo/CL_4047025`

type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508`

Caroline-99 Oct 24, 2024 •

edited

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Caroline-99 Oct 24, 2024 •

edited

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