Addresses #1827 NTR peg cell #1828

aleixpuigb · 2023-02-02T15:22:45Z

Resolves #1827 NTR peg cell

Addresses 1827 NTR peg cell

src/ontology/cl-edit.owl

ghost · 2023-02-03T09:20:26Z

src/ontology/cl-edit.owl

+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4033014 "intercalary cell")
+AnnotationAssertion(rdfs:label obo:CL_4033014 "peg cell")
+SubClassOf(obo:CL_4033014 obo:CL_0000151)
+SubClassOf(obo:CL_4033014 obo:CL_1001591)


Is there evidence to support this assertion?

Isn't this definitional? 'fallopian tube epithelium' = 'oviduct epithelium' in Uberon. This seems reasonable given:

https://en.wikipedia.org/wiki/Fallopian_tube

However, Uberon structure looks quite broken here as the term appears to cover many different epithelia of the female reproductive system.

TODO Add Uberon ticket on this. Might be complicated due to cross-species nature of ontology.

As noted above, PMID:22911892 seems to only investigate the fallopian tube epithelium as opposed to whole oviduct. Is there a reference (other than BTO) that reports this cell in other locations of the oviduct?

ghost

Please see inline comments.

src/ontology/cl-edit.owl

ghost

See inline comments.

dosumis

Requested changes in the comments

dosumis · 2023-02-03T11:13:57Z

src/ontology/cl-edit.owl

+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4033014 "intercalary cell")
+AnnotationAssertion(rdfs:label obo:CL_4033014 "peg cell")
+SubClassOf(obo:CL_4033014 obo:CL_0000151)
+SubClassOf(obo:CL_4033014 obo:CL_1001591)


Isn't this definitional? 'fallopian tube epithelium' = 'oviduct epithelium' in Uberon. This seems reasonable given:

https://en.wikipedia.org/wiki/Fallopian_tube

However, Uberon structure looks quite broken here as the term appears to cover many different epithelia of the female reproductive system.

TODO Add Uberon ticket on this. Might be complicated due to cross-species nature of ontology.

src/ontology/cl-edit.owl

anitacaron · 2023-02-07T10:41:43Z

#gogoeditdiff

github-actions · 2023-02-07T10:43:16Z

Your branch is 13 commit/s behind, please update your branch.

anitacaron · 2023-02-07T10:51:06Z

#gogoeditdiff

ghost · 2023-02-07T10:52:11Z

src/ontology/cl-edit.owl

+AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033014 <https://orcid.org/0000-0001-6677-8489>)
+AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033014 "2023-02-02T15:07:12Z"^^xsd:dateTime)
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4033014 "FTE stem-like cell")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22911892"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4033014 "FTESC")


Consider adding has_synonym_type "abbreviation". Can refer to CL:4030035 'dental pulp stem cell' for an example.

src/ontology/cl-edit.owl

github-actions · 2023-02-07T10:56:03Z

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/2023-02-09/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/2023-02-09/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`

Added

CL_4033014 comment "In vitro evidence supports a stem-cell/regenerative function for these cells"
- database_cross_reference "PMID:22911892"
CL_4033014 has_exact_synonym "fallopian tube epithelial stem-like cell"
- database_cross_reference "PMID:22911892"
CL_4033014 date "2023-02-02T15:07:12Z"^^dateTime
CL_4033014 has_exact_synonym "intercalary cell"
- database_cross_reference "PMID:22911892"
CL_4033014 definition "A small, narrow, peg-shaped epithelial cell with little cytoplasm that is part of oviduct epithelium. This cell is rarer than the ciliated and secretory epithelial cells of the fallopian tube epithelium and is often found intercalated between them. Peg cells are generally distributed basally along the epithelium and have been found in high concentrations at the fimbriated, distal end of the fallopian tube in humans. It may have a regenerative/stem-cell function. In humans, markers include EPCAM, CD44, and ITGA6."
- database_cross_reference "PMID:30023181"
- database_cross_reference "PMID:2210508"
- database_cross_reference "PMID:22911892"
CL_4033014 label "peg cell"
CL_4033014 has_exact_synonym "FTE stem-like cell"
- database_cross_reference "PMID:22911892"
CL_4033014 has_exact_synonym "FTESC"
- has_synonym_type abbreviation
- database_cross_reference "PMID:22911892"
CL_4033014 contributor 0000-0001-6677-8489
Class: CL_4033014
CL_4033014 SubClassOf epithelial cell

github-actions · 2023-02-07T10:56:06Z

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

CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`

Added

CL_4033014 comment "In vitro evidence supports a stem-cell/regenerative function for these cells"^^string
- database_cross_reference "PMID:22911892"^^string
CL_4033014 has_exact_synonym "fallopian tube epithelial stem-like cell"
- database_cross_reference "PMID:22911892"^^string
CL_4033014 date "2023-02-02T15:07:12Z"^^dateTime
CL_4033014 has_exact_synonym "intercalary cell"
- database_cross_reference "PMID:22911892"^^string
CL_4033014 definition "A small, narrow, peg-shaped epithelial cell with little cytoplasm that is part of oviduct epithelium. This cell is rarer than the ciliated and secretory epithelial cells of the fallopian tube epithelium and is often found intercalated between them. Peg cells are generally distributed basally along the epithelium and have been found in high concentrations at the fimbriated, distal end of the fallopian tube in humans. It may have a regenerative/stem-cell function. In humans, markers include EPCAM, CD44, and ITGA6."^^string
- database_cross_reference "PMID:22911892"^^string
- database_cross_reference "PMID:2210508"^^string
- database_cross_reference "PMID:30023181"^^string
CL_4033014 label "peg cell"^^string
CL_4033014 has_exact_synonym "FTE stem-like cell"
- database_cross_reference "PMID:22911892"^^string
CL_4033014 has_exact_synonym "FTESC"
- database_cross_reference "PMID:22911892"^^string
- has_synonym_type abbreviation
CL_4033014 contributor 0000-0001-6677-8489
Class: CL_4033014
CL_4033014 SubClassOf part_of some oviduct epithelium
CL_4033014 SubClassOf epithelial cell

src/ontology/cl-edit.owl

ghost

See inline comments.

…ell-ontology into 1827_NTR_peg_cell

ghost

See comment on text def.
Otherwise OK.

aleixpuigb · 2023-02-09T13:40:14Z

#gogoeditdiff

aleixpuigb · 2023-02-09T13:59:03Z

#gogoeditdiff

Addresses 1827 NTR peg cell

b76c149

Addresses 1827 NTR peg cell

aleixpuigb requested a review from a user February 2, 2023 15:22

aleixpuigb self-assigned this Feb 2, 2023

Update cl-edit.owl

1b31c9d

aleixpuigb added new term request HuBMAP Needed/useful for HuBMAP labels Feb 2, 2023

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aleixpuigb added 2 commits February 3, 2023 10:17

Update cl-edit.owl

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aleixpuigb added 2 commits February 3, 2023 12:24

Update cl-edit.owl

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Update cl-edit.owl

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aleixpuigb requested a review from a user February 7, 2023 10:26

Merge branch 'master' into 1827_NTR_peg_cell

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aleixpuigb added 2 commits February 7, 2023 13:29

Update cl-edit.owl

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Merge branch '1827_NTR_peg_cell' of https:/obophenotype/c…

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…ell-ontology into 1827_NTR_peg_cell

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Merge branch 'master' into 1827_NTR_peg_cell

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aleixpuigb requested a review from dosumis February 9, 2023 14:00

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aleixpuigb merged commit 2a23ea6 into master Feb 9, 2023

aleixpuigb deleted the 1827_NTR_peg_cell branch February 9, 2023 20:13

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Addresses #1827 NTR peg cell #1828

Addresses #1827 NTR peg cell #1828

aleixpuigb commented Feb 2, 2023

ghost Feb 3, 2023

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edited by aleixpuigb

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Ontology comparison

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Ontology imports

Ontology annotations

CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`

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Ontology imports

Ontology annotations

CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`

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aleixpuigb commented Feb 9, 2023

aleixpuigb commented Feb 9, 2023

Addresses #1827 NTR peg cell #1828

Addresses #1827 NTR peg cell #1828

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aleixpuigb commented Feb 2, 2023

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Ontology comparison

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Right

Ontology imports

Ontology annotations

CL_4033014 http://purl.obolibrary.org/obo/CL_4033014

Added

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Ontology comparison

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Ontology imports

Ontology annotations

CL_4033014 http://purl.obolibrary.org/obo/CL_4033014

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aleixpuigb commented Feb 9, 2023

aleixpuigb commented Feb 9, 2023

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CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`

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CL_4033014 `http://purl.obolibrary.org/obo/CL_4033014`