Add episcleral vein term (UBERON:7770011)#3582
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Co-authored-by: cmungall <50745+cmungall@users.noreply.github.com>
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
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Ontology importsOntology annotationsepiscleral vein
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsepiscleral vein
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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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@copilot - looks good apart from addition of new file under /terms. Please revert this. The only file that should be edited is src/ontology/uberon-edit.obo. |
- Changed episcleral vein ID from UBERON:7770009 to UBERON:7770011 - Removed terms/UBERON_7770009.obo file as requested - Fixed duplicate ID conflict with kidney interpolar region term @dragon-ai-agent Co-authored-by: dosumis <112839+dosumis@users.noreply.github.com>
@dragon-ai-agent Co-authored-by: dosumis <112839+dosumis@users.noreply.github.com>
Fixed! I've removed the terms/UBERON_7770009.obo file and also corrected a duplicate ID issue I discovered. The episcleral vein term now uses UBERON:7770011 instead of the conflicting UBERON:7770009 (which was already taken by kidney interpolar region). Only src/ontology/uberon-edit.obo is now modified as requested. Commit: ff2bb82 |
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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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@matentzn with the exception of reverting gitignore, which adds the line 'tools/', this should be ready to rebase. |
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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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@aleixpuigb review, fix QC, merge. |
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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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Claude finished @aleixpuigb's task in 3m 56s —— View job PR Review: Add episcleral vein term (UBERON:7770011)Todo list:
Review checklist
FindingsThe new term UBERON:7770011 episcleral vein is correctly formed and faithfully implements the NTR from issue #1680: The CI diff showing No 🔵 SUGGESTION (non-blocking): No PMID in the definition — the requester didn't supply one and the Wikipedia article on the episcleral layer is the main available reference. A PMID could be added in a follow-up. PR is approved and ready to merge. |
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Review checklist
- Hierarchy and parents are consistent —
UBERON:0009141(craniocervical region vein) is a valid, safe parent;UBERON:0010292(episcleral layer of eyeball) correctly used forpart_of - Definitions and supporting references look adequate — definition matches the NTR request verbatim;
FMA:51800andWikipedia:Episcleral_layerare the references the requester provided - Obsolete or replacement handling is safe — N/A (new term only)
- OBO and ODK conventions appear preserved — contributor ORCID, date, term_tracker_item, created_by all present; only
src/ontology/uberon-edit.obois modified - No obvious CI, auth, or workflow regression — no .gitignore changes in this PR;
tools/directory is untracked but not committed
Summary
The new term UBERON:7770011 episcleral vein is correctly formed and faithfully implements the NTR from issue #1680. The CI diff in the PR comments showing UBERON_7770009 is stale — it ran before the ID fix was committed; the actual file now uses UBERON:7770011.
One minor note: no PMID is present in the definition (the requester did not supply one), and Wikipedia:Episcleral_layer references the episcleral layer article rather than a dedicated vein article. This is acceptable given that the vein is defined in that context and FMA:51800 provides a formal anatomy reference. A PMID could be added in a follow-up if needed.
Ready to merge. @aleixpuigb or @matentzn can proceed with merging.
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Claude finished @aleixpuigb's task in 2m 32s —— View job PR Review: Add episcleral vein term (UBERON:7770011)Todo list:
Review checklist
FindingsThe new term as it exists in the file: ID is correct: UBERON:7770011 is confirmed in the file. UBERON:7770009 already exists as "kidney interpolar region" — the ID fix was correctly applied. The stale CI diff in PR comments (showing 7770009) reflects the pre-fix state and can be ignored. Hierarchy: Only one file modified: All required metadata present: contributor ORCID, date, term_tracker_item, created_by — all present and well-formed. 🔵 SUGGESTION (non-blocking): Definition cites PR is approved and ready to merge. |
There was a problem hiding this comment.
Review checklist
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Summary
Term UBERON:7770011 episcleral vein is correctly formed. Verified in the actual file:
- ID UBERON:7770011 is correct (UBERON:7770009 exists as 'kidney interpolar region' — ID fix was properly applied; stale CI diff showing 7770009 can be ignored)
- Parent
is_a UBERON:0009141(craniocervical region vein) is anatomically appropriate part_of UBERON:0010292(episcleral layer of eyeball) is correct — the episcleral layer definition explicitly describes the episcleral vascular plexus- Only
src/ontology/uberon-edit.obois modified; no .gitignore changes; tools/ is untracked but not committed - All required metadata present: contributor ORCID, date, term_tracker_item, created_by
🔵 SUGGESTION (non-blocking): No PMID in definition — FMA:51800 and Wikipedia:Episcleral_layer are acceptable references. A PMID could be added in a follow-up.
Ready to merge.
This PR adds a new term "episcleral vein" to the UBERON ontology as requested in issue #1680.
New Term Details
UBERON:7770011 - episcleral vein
Changes Made
src/ontology/uberon-edit.obofollowing existing patternsValidation
The new term has been validated using the existing
obo-grep.pltool and confirmed to:Fixes #1680.
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