Fixes #3427 NTR- epithelium of anorectum #3430

Caroline-99 · 2024-11-19T12:43:04Z

Added a new term.

Needed for CL #2674

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

github-actions

Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

github-actions · 2025-01-17T02:09:25Z

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

cmungall · 2025-01-17T03:22:03Z

src/ontology/uberon-edit.obo

 synonymtypedef: SENSU "taxonomic disambiguation"
 synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns"
 default-namespace: uberon
-idspace: EFO http://www.ebi.ac.uk/efo/EFO_ 


can you check which version of Protege you are using? These should not disappear, it leads me to think you're using an older version with an older owlapi

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

github-actions · 2025-03-10T02:01:18Z

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

github-actions · 2025-04-10T02:23:23Z

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Added a new term.

…eference

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

aleixpuigb · 2025-05-08T09:42:49Z

src/ontology/uberon-edit.obo

 synonymtypedef: SENSU "taxonomic disambiguation"
 synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns"
 default-namespace: uberon
+idspace: EFO http://www.ebi.ac.uk/efo/EFO_ 


@gouttegd is this addition ok? Thanks!

Thanks for asking!

Yes, this is normal. In fact that line had already been there before, but it had been removed at some point because someone has edited the ontology using a slightly older version of Protégé.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

gouttegd · 2025-05-12T12:44:33Z

#gogoeditdiff

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

gouttegd · 2025-05-12T14:31:54Z

#gogoeditdiff

github-actions · 2025-05-12T14:43:58Z

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/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2025-05-12/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2025-05-12/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

epithelium of anorectum `http://purl.obolibrary.org/obo/UBERON_8850001`

Added

epithelium of anorectum contributor 0009-0000-8480-9277
epithelium of anorectum id "UBERON:8850001"
epithelium of anorectum date "2024-11-18T15:45:29Z"^^dateTime
epithelium of anorectum IAO_0000115 "The epithelium that lines the anorectum."
- hasDbXref "PMID:27042391"
epithelium of anorectum hasOBONamespace "uberon"
epithelium of anorectum label "epithelium of anorectum"
epithelium of anorectum hasExactSynonym "anorectal epithelium"
- hasDbXref "PMID:27042391"
Class: epithelium of anorectum
epithelium of anorectum EquivalentTo epithelium and (BFO_0000050 some anorectum)
epithelium of anorectum SubClassOf epithelium of large intestine
epithelium of anorectum SubClassOf BFO_0000050 some anorectum

obsolete median fin skeleton `http://purl.obolibrary.org/obo/UBERON_0002543`

Removed

obsolete median fin skeleton consider EFO_0000950

Added

obsolete median fin skeleton consider EFO_0000950

obsolete tuber `http://purl.obolibrary.org/obo/UBERON_0000380`

Removed

obsolete tuber consider EFO_0001015

Added

obsolete tuber consider EFO_0001015

github-actions · 2025-05-12T14:44:01Z

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

Ontology comparison

Left

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

Right

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

Ontology imports

Ontology annotations

epithelium of anorectum `http://purl.obolibrary.org/obo/UBERON_8850001`

Added

epithelium of anorectum contributor 0009-0000-8480-9277
epithelium of anorectum id "UBERON:8850001"^^string
epithelium of anorectum date "2024-11-18T15:45:29Z"^^dateTime
epithelium of anorectum definition "The epithelium that lines the anorectum."^^string
- database_cross_reference "PMID:27042391"^^string
epithelium of anorectum has_obo_namespace "uberon"^^string
epithelium of anorectum label "epithelium of anorectum"^^string
epithelium of anorectum has_exact_synonym "anorectal epithelium"^^string
- database_cross_reference "PMID:27042391"^^string
Class: epithelium of anorectum
epithelium of anorectum EquivalentTo epithelium and (part of some anorectum)

obsolete median fin skeleton `http://purl.obolibrary.org/obo/UBERON_0002543`

Removed

obsolete median fin skeleton consider EFO_0000950

Added

obsolete median fin skeleton consider EFO_0000950

obsolete tuber `http://purl.obolibrary.org/obo/UBERON_0000380`

Removed

obsolete tuber consider EFO_0001015

Added

obsolete tuber consider EFO_0001015

github-actions · 2025-06-12T02:42:54Z

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

Caroline-99 linked an issue Nov 19, 2024 that may be closed by this pull request

epithelium of anorectum #3427

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github-actions bot requested a review from cmungall November 19, 2024 12:46

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Caroline-99 added 4 commits April 23, 2025 23:21

Fixes #3427

d997659

Added a new term.

Update uberon-edit.obo

e3ab9a6

Update uberon-edit.obo

332d073

Added a cross reference for the definition and exact synonym with a r…

e203aeb

…eference

cmungall force-pushed the 3427-epithelium-of-anorectum branch from b3200ac to e203aeb Compare April 24, 2025 03:21

github-actions bot requested changes Apr 24, 2025

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Merge branch 'master' into 3427-epithelium-of-anorectum

be8d591

github-actions bot requested changes Apr 28, 2025

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aleixpuigb reviewed May 8, 2025

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aleixpuigb approved these changes May 8, 2025

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Merge branch 'master' into 3427-epithelium-of-anorectum

d0f7495

github-actions bot requested changes May 8, 2025

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gouttegd approved these changes May 12, 2025

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Merge branch 'master' into 3427-epithelium-of-anorectum

76d6b43

github-actions bot requested changes May 12, 2025

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github-actions bot added the unreviewed label Jun 12, 2025

Fixes #3427 NTR- epithelium of anorectum #3430

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Fixes #3427 NTR- epithelium of anorectum #3430

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gouttegd commented May 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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gouttegd commented May 12, 2025

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Ontology comparison

Left

Right

Ontology imports

Ontology annotations

epithelium of anorectum http://purl.obolibrary.org/obo/UBERON_8850001

Added

obsolete median fin skeleton http://purl.obolibrary.org/obo/UBERON_0002543

Removed

Added

obsolete tuber http://purl.obolibrary.org/obo/UBERON_0000380

Removed

Added

Uh oh!

github-actions bot commented May 12, 2025

Ontology comparison

gouttegd commented May 12, 2025 •

edited

Loading

epithelium of anorectum `http://purl.obolibrary.org/obo/UBERON_8850001`

obsolete median fin skeleton `http://purl.obolibrary.org/obo/UBERON_0002543`

obsolete tuber `http://purl.obolibrary.org/obo/UBERON_0000380`

epithelium of anorectum `http://purl.obolibrary.org/obo/UBERON_8850001`

obsolete median fin skeleton `http://purl.obolibrary.org/obo/UBERON_0002543`

obsolete tuber `http://purl.obolibrary.org/obo/UBERON_0000380`