BEST4 enterocyte and subtypes #2465

JABelfiore · 2024-07-25T13:42:11Z

class hierarchy revision and 2 subclasses added

dosumis · 2024-07-25T14:27:05Z

#gogoeditdiff

github-actions · 2024-07-25T14:32:19Z

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/2024-07-25/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/2024-07-25/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047002`

Added

BEST4+ colonocyte date "2024-07-25T13:21:19Z"^^dateTime
BEST4+ colonocyte contributor 0009-0005-7919-4905
BEST4+ colonocyte label "BEST4+ colonocyte"
BEST4+ colonocyte definition "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference "PMID:34497389"
Class: BEST4+ colonocyte
BEST4+ colonocyte SubClassOf enterocyte of colon
BEST4+ colonocyte SubClassOf BEST4+ enterocyte

BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4030026`

Removed

BEST4+ enterocyte label "BEST4+ intestinal epithelial cell, human"
BEST4+ enterocyte definition "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference 0000-0002-7431-4139
- database_cross_reference "PMID:35176508"
BEST4+ enterocyte SubClassOf gut absorptive cell

Added

BEST4+ enterocyte label "BEST4+ enterocyte"
BEST4+ enterocyte definition "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference 0000-0002-7431-4139
- database_cross_reference "PMID:35176508"
BEST4+ enterocyte SubClassOf enterocyte

small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047001`

Added

small intestine BEST4+ enterocyte date "2024-07-25T13:05:50Z"^^dateTime
small intestine BEST4+ enterocyte label "small intestine BEST4+ enterocyte"
small intestine BEST4+ enterocyte contributor 0009-0005-7919-4905
small intestine BEST4+ enterocyte definition "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference "PMID:34497389"
Class: small intestine BEST4+ enterocyte
small intestine BEST4+ enterocyte SubClassOf epithelial cell of small intestine
small intestine BEST4+ enterocyte SubClassOf BEST4+ enterocyte

github-actions · 2024-07-25T14:32:22Z

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

BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047002`

Added

BEST4+ colonocyte date "2024-07-25T13:21:19Z"^^dateTime
BEST4+ colonocyte contributor 0009-0005-7919-4905
BEST4+ colonocyte label "BEST4+ colonocyte"
BEST4+ colonocyte definition "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference "PMID:34497389"
Class: BEST4+ colonocyte
BEST4+ colonocyte SubClassOf part of some colon
BEST4+ colonocyte SubClassOf BEST4+ enterocyte
BEST4+ colonocyte SubClassOf expresses some bestrophin-4 (human)

BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4030026`

Removed

BEST4+ enterocyte label "BEST4+ intestinal epithelial cell, human"
BEST4+ enterocyte definition "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference 0000-0002-7431-4139
- database_cross_reference "PMID:35176508"
BEST4+ enterocyte SubClassOf gut absorptive cell

Added

BEST4+ enterocyte label "BEST4+ enterocyte"
BEST4+ enterocyte definition "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference 0000-0002-7431-4139
- database_cross_reference "PMID:35176508"
BEST4+ enterocyte SubClassOf enterocyte

small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047001`

Added

small intestine BEST4+ enterocyte date "2024-07-25T13:05:50Z"^^dateTime
small intestine BEST4+ enterocyte label "small intestine BEST4+ enterocyte"
small intestine BEST4+ enterocyte contributor 0009-0005-7919-4905
small intestine BEST4+ enterocyte definition "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."
- database_cross_reference "PMID:24223998"
- database_cross_reference "PMID:34497389"
Class: small intestine BEST4+ enterocyte
small intestine BEST4+ enterocyte SubClassOf expresses some bestrophin-4 (human)
small intestine BEST4+ enterocyte SubClassOf BEST4+ enterocyte
small intestine BEST4+ enterocyte SubClassOf part of some small intestine

dosumis · 2024-07-25T16:15:05Z

Looks good, but better to make part relationships to epithelium of colon/small intestine.

Also, there is some potential material on function in source papers that could go in extended description.

anitacaron · 2024-07-26T06:55:42Z

Please always provide a descriptive PR title to clarify the changes in the release notes. 😄

AvolaAmg

Please see in line comments

src/ontology/cl-edit.owl

AvolaAmg · 2024-07-26T13:46:09Z

src/ontology/cl-edit.owl


-AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")


consider to add the broad synonym
BEST4+ epithelial cell https://www.nature.com/articles/s41586-021-03852-1
BEST4+ cell
and
The related synonym
BEST4-expressing enterocyte (same paper)

we decided to add as exact

@JABelfiore Have these terms been added as exact synonyms? I can only see BEST4+ intestinal epithelial cell, human as exact synonym

logical definition updated best4

…thelial-cell-human

src/ontology/cl-edit.owl

Caroline-99 · 2024-08-19T15:39:58Z

The QC is still failing. This seems to be because each of these classes (CL:4047001 and CL:4047002) is associated with multiple, conflicting definitions. I think @JABelfiore you might need to change the CL Ids manually.
@aleixpuigb could you please check that?

aleixpuigb · 2024-08-19T15:41:50Z

The QC is still failing. This seems to be because each of these classes (CL:4047001 and CL:4047002) is associated with multiple, conflicting definitions. I think @JABelfiore you might need to change the CL Ids manually. @aleixpuigb could you please check that?

That's correct, Those ID were used for cycling cells.

CL IDs manually edited to prevent equivalent classes

…thelial-cell-human

Caroline-99 · 2024-09-06T09:49:59Z

#gogoeditdiff

Caroline-99 · 2024-09-06T09:54:11Z

The QC is still failing. This seems to be because each of these classes (CL:4047001 and CL:4047002) is associated with multiple, conflicting definitions. I think @JABelfiore you might need to change the CL Ids manually. @aleixpuigb could you please check that?

@aleixpuigb it seems that all the cells that Jasmine added have been removed. I can't find them anymore on this branch. I think this might have happened when Jasmine was trying to resolve conflicts.

…thelial-cell-human

@JABelfiore

Adding back BEST4 enterocyte types - recovered from earlier commits - using higher IDs from @JABelfiore ID range (+50).

fixed IDs and reserialized

- Fixed IDs - Tweaks to textual and logical defs - renamed enterocyte of colon to colonocyte for consistency

dosumis · 2024-09-13T17:47:15Z

#gogoeditdiff

need to get this out. I think good enough

class hierarchy revision

dd70a41

class hierarchy revision and 2 subclasses added

JABelfiore linked an issue Jul 25, 2024 that may be closed by this pull request

[Class hierarchy] BEST4+ intestinal epithelial cell, human #2410

Closed

JABelfiore assigned JABelfiore and AvolaAmg and unassigned AvolaAmg Jul 25, 2024

JABelfiore requested a review from AvolaAmg July 25, 2024 13:42

AvolaAmg requested a review from anitacaron July 26, 2024 13:06

AvolaAmg reviewed Jul 26, 2024

View reviewed changes

Fixes #2410

ec0bb2e

logical definition updated best4

dosumis changed the title ~~class hierarchy revision~~ BEST4 enterocyte and subtypes Aug 2, 2024

dosumis and others added 3 commits August 2, 2024 14:44

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

91ecd54

…thelial-cell-human

related synonym added

9d51823

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

3e2f3da

…thelial-cell-human

JABelfiore requested a review from Caroline-99 August 6, 2024 13:35

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

00c5f36

…thelial-cell-human

Caroline-99 previously requested changes Aug 19, 2024

View reviewed changes

src/ontology/cl-edit.owl Outdated Show resolved Hide resolved

JABelfiore added 2 commits August 29, 2024 15:05

CL ID updated

425230d

CL IDs manually edited to prevent equivalent classes

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

dcc785e

…thelial-cell-human

JABelfiore requested a review from Caroline-99 August 29, 2024 14:16

JABelfiore and others added 3 commits August 30, 2024 13:18

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

79f889b

…thelial-cell-human

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

e44a3cb

…thelial-cell-human

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

ffce836

…thelial-cell-human

dosumis added 4 commits September 13, 2024 16:22

Merge branch 'master' into 2410-class-hierarchy-best4+-intestinal-epi…

1a4b12d

…thelial-cell-human

Update cl-edit.owl

e6cf640

Adding back BEST4 enterocyte types - recovered from earlier commits - using higher IDs from @JABelfiore ID range (+50).

Update cl-edit.owl

0cb956a

fixed IDs and reserialized

Update cl-edit.owl

7c4485c

- Fixed IDs - Tweaks to textual and logical defs - renamed enterocyte of colon to colonocyte for consistency

dosumis mentioned this pull request Sep 13, 2024

Complete NTRs & edits required for mapping of Gut Cell Atlas terms #2560

Open

20 tasks

dosumis approved these changes Sep 14, 2024

View reviewed changes

dosumis merged commit 4adcd94 into master Sep 14, 2024
1 check passed

dosumis deleted the 2410-class-hierarchy-best4+-intestinal-epithelial-cell-human branch September 14, 2024 09:22


		AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")
		AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-7431-4139>) Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:35176508") obo:IAO_0000115 obo:CL_4030026 "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels.")

BEST4 enterocyte and subtypes #2465

BEST4 enterocyte and subtypes #2465

Conversation

JABelfiore commented Jul 25, 2024

dosumis commented Jul 25, 2024

github-actions bot commented Jul 25, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

BEST4+ colonocyte http://purl.obolibrary.org/obo/CL_4047002

Added

BEST4+ enterocyte http://purl.obolibrary.org/obo/CL_4030026

Removed

Added

small intestine BEST4+ enterocyte http://purl.obolibrary.org/obo/CL_4047001

Added

github-actions bot commented Jul 25, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

BEST4+ colonocyte http://purl.obolibrary.org/obo/CL_4047002

Added

BEST4+ enterocyte http://purl.obolibrary.org/obo/CL_4030026

Removed

Added

small intestine BEST4+ enterocyte http://purl.obolibrary.org/obo/CL_4047001

Added

dosumis commented Jul 25, 2024

anitacaron commented Jul 26, 2024

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Caroline-99 Aug 19, 2024

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Caroline-99 commented Aug 19, 2024

aleixpuigb commented Aug 19, 2024

Caroline-99 commented Sep 6, 2024

Caroline-99 commented Sep 6, 2024

dosumis commented Sep 13, 2024

BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047002`

BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4030026`

small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047001`

BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047002`

BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4030026`

small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047001`