Fixes #3640 Update eyelid textual definition#3641
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Fixes #3640 to correctly classify eyelid as a facial skin
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#gogoeditdiff |
aleixpuigb
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Pull request overview
This PR attempts to fix issue #3640 by reclassifying the eyelid from "organ part" to "zone of skin". However, this change is semantically incorrect based on the anatomical composition of the eyelid and established ontology patterns.
Key Changes:
- Changed the parent classification of eyelid (UBERON:0001711) from "organ part" (UBERON:0000064) to "zone of skin" (UBERON:0000014)
aleixpuigb
changed the title
- Changed is_a from organ part to external soft tissue zone (UBERON:0034929) - Added has_part relationships for skin of eyelid and palpebral conjunctiva - Follows pattern established by prepuce for multi-tissue surface structures - Addresses feedback on PR #3641 about semantic classification @dragon-ai-agent Co-authored-by: dosumis <112839+dosumis@users.noreply.github.com>
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Looks great but we need to be careful about species specificity - see https://chatgpt.com/share/695be87e-5674-800f-8d22-1862ee3c772e Maybe have a general term eyelid for vertebrates and keep this one for mammals, but indicate parenthetically bits that only apply to humans or primates. Potential general term: Edits to this term def: A movable anterior covering of the eye composed of skin, muscle, dense connective tissue (tarsal plate in humans, primates) with embedded meibomian glands, and palpebral conjunctiva; functions to protect the eyeball, distribute the tear film, and maintain the eyelash margin where this is present (humans, primates and some carnivores).
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I have made the term general for any species with eyelids. I am not sure if we need a specific term for mammals/humans. |
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We need to merge #3652 first to solve the problems. |
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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 40s —— View job PR Review: Fixes #3640 Update eyelid textual definitionChecklist
SummaryThe actual change (from the diff): -def: "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane." [http://orcid.org/0000-0002-6601-2165]
+def: "A movable or semi-movable ocular covering that protects the eye and contributes to surface maintenance; structure and composition vary widely among vertebrate species." [http://orcid.org/0000-0002-6601-2165, PMID:29493929]This is only a textual definition change — no hierarchy or logical axioms are modified. The This is a clear improvement. The old definition's characterization of the eyelid as a "fold of skin" was anatomically incorrect — the eyelid is a composite structure containing skin, subcutaneous connective tissue, striated muscle (orbicularis), fibrous layer / tarsal plate, smooth muscle, and palpebral conjunctiva (all documented in the existing The Issues🔵 SUGGESTION: PMID scope is narrower than the definition's cross-vertebrate claim PMID:29493929 (Cochran et al., "Anatomy, Head and Neck: Eyelid", StatPearls) is a valid human clinical anatomy reference. It supports the core definition (movable ocular covering, eye protection, surface maintenance) but does not address vertebrate variation. The phrase "structure and composition vary widely among vertebrate species" is a general biological fact not covered by this PMID. Ideally a comparative vertebrate anatomy source would be added alongside it. That said, the PMID does support the primary functional definition and this is not a blocker. 🔵 SUGGESTION: Add Per the UBERON curation guide, terms should link back to the issue being addressed. The eyelid term is missing a RecommendationApproved. The change is anatomically correct and clearly improves the definition. The hierarchy and OBO conventions are intact. The above points are suggestions, not blockers. |
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The definition change from 'fold of skin' to the more general cross-vertebrate definition is anatomically correct and an improvement. The is_a: organ part hierarchy is unchanged. Two minor suggestions: (1) the cited PMID:29493929 (StatPearls, human-specific) does not cover the cross-vertebrate variation claim — consider adding a comparative anatomy source; (2) a term_tracker_item linking to issue #3640 could be added. Neither is a blocker. Approve.
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Claude finished @aleixpuigb's task in 2m 18s —— View job PR Review: Fixes #3640 Update eyelid textual definitionChecklist
SummaryThe actual change (from the diff): -def: "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane." [http://orcid.org/0000-0002-6601-2165]
+def: "A movable or semi-movable ocular covering that protects the eye and contributes to surface maintenance; structure and composition vary widely among vertebrate species." [http://orcid.org/0000-0002-6601-2165, PMID:29493929]This is only a textual definition change — no hierarchy or logical axioms are modified. The The old "fold of skin" characterization was anatomically incorrect. The eyelid is a composite multi-tissue structure documented in the existing Issues🔵 SUGGESTION: Missing Per UBERON curation guidelines, terms should link to the issue being addressed. Adding the following would be appropriate: 🔵 SUGGESTION: PMID scope narrower than the cross-vertebrate claim PMID:29493929 (Cochran et al., StatPearls) is a human clinical anatomy reference. It supports the core functional definition (movable ocular covering, eye protection, surface maintenance) but does not address vertebrate variation. The claim "structure and composition vary widely among vertebrate species" is not directly backed by this citation. Consider adding a comparative vertebrate anatomy source. Not a blocker. 🔵 SUGGESTION: Examples were informative in the old definition The old definition included "Examples: upper eyelid, lower eyelid, nictitating membrane" which usefully clarified scope. Consider retaining these as a RecommendationApproved. The change is anatomically correct and a clear improvement. The hierarchy and OBO conventions are intact. The above points are suggestions only, not blockers. |
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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
The actual change is a textual definition improvement only — no hierarchy or logical axioms are modified:
-def: "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane." [http://orcid.org/0000-0002-6601-2165]
+def: "A movable or semi-movable ocular covering that protects the eye and contributes to surface maintenance; structure and composition vary widely among vertebrate species." [http://orcid.org/0000-0002-6601-2165, PMID:29493929]The is_a: UBERON:0000064 ! organ part parent is correctly preserved. The old "fold of skin" characterization was anatomically incorrect — the eyelid is a composite structure containing 7 distinct layers (skin, subcutaneous connective tissue, striated muscle, submuscular connective tissue, fibrous layer/tarsal plate, smooth muscle, palpebral conjunctiva), as documented in the existing taxon_notes. The new definition correctly avoids this error and is appropriately general for a cross-species ontology. The inclusion of "semi-movable" correctly handles nictitating membranes in various species.
Suggestions (non-blocking):
🔵 SUGGESTION: term_tracker_item for issue #3640 is missing. Per UBERON curation guidelines, consider adding:
property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3640" xsd:anyURI
🔵 SUGGESTION: PMID:29493929 (StatPearls, Cochran et al.) is a human clinical anatomy reference and does not cover cross-vertebrate variation. The phrase "structure and composition vary widely among vertebrate species" is not directly supported. Consider adding a comparative vertebrate anatomy source alongside this PMID. That said, the PMID does support the functional claims (ocular covering, eye protection, surface maintenance) and is not a blocker.
🔵 SUGGESTION: The old definition included examples ("Examples: upper eyelid, lower eyelid, nictitating membrane") that clarified scope. Consider retaining these as a comment or incorporating examples into the definition.
Approved. The change is anatomically correct and a clear improvement over the old definition.
Fixes #3640
The eyelid is a composite anatomical structure that is not solely composed by skin. This PR updates the definition to reflect this and provides a dbxref: