M cell and FAE partonomy update #2897

JABelfiore · 2025-01-10T16:10:33Z

both made part of peyer's patch epithelium

Caroline-99 · 2025-01-13T10:39:58Z

#gogoeditdiff

github-actions · 2025-01-13T10:45:51Z

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

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-01-14/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-01-14/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

M cell of gut `http://purl.obolibrary.org/obo/CL_0000682`

Removed

M cell of gut SubClassOf epithelial cell of alimentary canal

Added

M cell of gut SubClassOf intestinal epithelial cell
M cell of gut SubClassOf BFO_0000050 some UBERON_0004693

PR_000003490 `http://purl.obolibrary.org/obo/PR_000003490`

Removed

Class: PR_000003490

UBERON_0004693 `http://purl.obolibrary.org/obo/UBERON_0004693`

Added

Class: UBERON_0004693

granzyme H-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052032`

Removed

granzyme H-associated CD8 T cell comment "This cell type is significantly expanded in systemic lupus erythematosus (SLE) patients. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients."
- hasDbXref "PMID:35389781"
granzyme H-associated CD8 T cell IAO_0000115 "A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls."
- hasDbXref "PMID:35389781"
granzyme H-associated CD8 T cell date "2025-01-10T10:14:31Z"^^dateTime
granzyme H-associated CD8 T cell label "granzyme H-associated CD8 T cell"
granzyme H-associated CD8 T cell contributor 0009-0000-8480-9277
granzyme H-associated CD8 T cell contributor 0000-0002-3958-7465
granzyme H-associated CD8 T cell hasExactSynonym "granzyme H+ CD8 T cell"
- hasDbXref "PMID:35389781"
granzyme H-associated CD8 T cell hasRelatedSynonym "GZMH+ CD8+ T cell"
- hasSynonymType OMO_0003000
- hasDbXref "PMID:35389781"
Class: granzyme H-associated CD8 T cell
granzyme H-associated CD8 T cell EquivalentTo CD8-positive, alpha-beta memory T cell and (RO_0002292 some PR_000003490)
granzyme H-associated CD8 T cell SubClassOf CD8-positive, alpha-beta memory T cell
granzyme H-associated CD8 T cell SubClassOf RO_0002292 some PR_000003490

github-actions · 2025-01-13T10:45:52Z

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

M cell of gut `http://purl.obolibrary.org/obo/CL_0000682`

Removed

M cell of gut SubClassOf part of some digestive tract epithelium

Added

M cell of gut SubClassOf part of some Peyer's patch epithelium

PR_000003490 `http://purl.obolibrary.org/obo/PR_000003490`

Removed

Class: PR_000003490

granzyme H-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052032`

Removed

granzyme H-associated CD8 T cell comment "This cell type is significantly expanded in systemic lupus erythematosus (SLE) patients. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients."
- database_cross_reference "PMID:35389781"
granzyme H-associated CD8 T cell definition "A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls."
- database_cross_reference "PMID:35389781"
granzyme H-associated CD8 T cell date "2025-01-10T10:14:31Z"^^dateTime
granzyme H-associated CD8 T cell has exact synonym "granzyme H+ CD8 T cell"
- database_cross_reference "PMID:35389781"
granzyme H-associated CD8 T cell label "granzyme H-associated CD8 T cell"
granzyme H-associated CD8 T cell contributor 0009-0000-8480-9277
granzyme H-associated CD8 T cell contributor 0000-0002-3958-7465
granzyme H-associated CD8 T cell has_related_synonym "GZMH+ CD8+ T cell"
- database_cross_reference "PMID:35389781"
- has_synonym_type abbreviation
Class: granzyme H-associated CD8 T cell
granzyme H-associated CD8 T cell EquivalentTo CD8-positive, alpha-beta memory T cell and (expresses some PR_000003490)

Caroline-99 · 2025-01-13T10:59:13Z

src/ontology/cl-edit.owl

@@ -9506,7 +9506,7 @@ 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))


This looks good. You could also consider classifying M cells as part of follicle associated epithelium rather than part of Peyer's patch epithelium (PMID: 18081850) but either terms would work.

keeping as is as this was the change David requested

Caroline-99 · 2025-01-13T11:08:03Z

src/ontology/cl-edit.owl

@@ -9457,7 +9457,7 @@ SubClassOf(obo:CL_0000676 obo:CL_0000378)
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "JB:jb") obo:IAO_0000115 obo:CL_0000677 "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.")
 AnnotationAssertion(rdfs:label obo:CL_0000677 "gut absorptive cell")


I cannot see any changes to FAE (follicle associated enterocyte) - I believe it should be EquivalentTo enterocyte and part of some follicle associated epithelium. The uberon term will need to be imported into CL.

FAE has the anonymous ancestor part of some peyer's patch epithelium which is the edit requested

As agreed with @JABelfiore, part of some follicle associated epithelium will be added as a subclass to follicle associated epithelium enterocyte.

Caroline-99 · 2025-01-13T11:17:07Z

src/ontology/cl-edit.owl

@@ -9457,7 +9457,7 @@ SubClassOf(obo:CL_0000676 obo:CL_0000378)
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "JB:jb") obo:IAO_0000115 obo:CL_0000677 "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.")
 AnnotationAssertion(rdfs:label obo:CL_0000677 "gut absorptive cell")
 SubClassOf(obo:CL_0000677 obo:CL_0000000)
-SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001277))
+SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693))


gut absorptive cell is a grouping term for all enterocytes so it is not restricted to Peyer's patch epithelium (UBERON_0004693). I suggest changing it back to being part of intestinal epithelium (UBERON_0001277).

updated as suggested

…-epithelium

'part of' some 'intestinal epithelium'

dosumis · 2025-01-14T13:24:16Z

#gogoeditdiff

M cell and FAE partonomy update

f40a912

JABelfiore requested a review from Caroline-99 January 10, 2025 16:10

JABelfiore self-assigned this Jan 10, 2025

JABelfiore linked an issue Jan 10, 2025 that may be closed by this pull request

M cell should be part of Peyer's patch epithelium #2880

Open

Caroline-99 requested changes Jan 13, 2025

View reviewed changes

Caroline-99 and others added 2 commits January 13, 2025 11:34

Merge branch 'master' into 2880-m-cell-should-be-part-of-peyers-patch…

2379bd7

…-epithelium

partonomy gut absorptive cell update

fc6eb1a

'part of' some 'intestinal epithelium'

partonomy update FAE

d9a2bf7

		@@ -9457,7 +9457,7 @@ SubClassOf(obo:CL_0000676 obo:CL_0000378)
		AnnotationAssertion(Annotation(oboInOwl:hasDbXref "JB:jb") obo:IAO_0000115 obo:CL_0000677 "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.")
		AnnotationAssertion(rdfs:label obo:CL_0000677 "gut absorptive cell")

M cell and FAE partonomy update #2897

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M cell and FAE partonomy update #2897

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JABelfiore commented Jan 10, 2025

Caroline-99 commented Jan 13, 2025

github-actions bot commented Jan 13, 2025 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

M cell of gut http://purl.obolibrary.org/obo/CL_0000682

Removed

Added

PR_000003490 http://purl.obolibrary.org/obo/PR_000003490

Removed

UBERON_0004693 http://purl.obolibrary.org/obo/UBERON_0004693

Added

granzyme H-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052032

Removed

github-actions bot commented Jan 13, 2025 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

M cell of gut http://purl.obolibrary.org/obo/CL_0000682

Removed

Added

PR_000003490 http://purl.obolibrary.org/obo/PR_000003490

Removed

granzyme H-associated CD8 T cell http://purl.obolibrary.org/obo/CL_4052032

Removed

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Caroline-99 Jan 14, 2025 • edited Loading

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dosumis commented Jan 14, 2025

github-actions bot commented Jan 13, 2025 •

edited

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M cell of gut `http://purl.obolibrary.org/obo/CL_0000682`

PR_000003490 `http://purl.obolibrary.org/obo/PR_000003490`

UBERON_0004693 `http://purl.obolibrary.org/obo/UBERON_0004693`

granzyme H-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052032`

github-actions bot commented Jan 13, 2025 •

edited

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M cell of gut `http://purl.obolibrary.org/obo/CL_0000682`

PR_000003490 `http://purl.obolibrary.org/obo/PR_000003490`

granzyme H-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052032`

Caroline-99 Jan 14, 2025 •

edited

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