NTR: add collagen band (UBERON:1200005)#3728
Conversation
Adds new term for collagen band as requested in issue #3727. - ID: UBERON:1200005 - Name: collagen band - Definition: "A band-shaped collection of collagen fibrils forming a distinct layer beneath an epithelium." - Parent: UBERON:0011860 (collection of collagen fibrils) - Synonyms: subepithelial collagen band, collagenous band, subepithelial collagen layer, superficial subepithelial collagen layer, subepithelial collagenous band - References: PMID:19295410 (Leung et al. 2009, Collagenous gastritis) and PMID:37022603 (scoping review, collagenous gastritis) - Contributor: Aleix Puig-Barbé (ORCID 0000-0001-6677-8489) Note: the original issue cited PMID:25216277 as definition source, but that PMID maps to an unrelated paper on transoral nasopharyngectomy. The two PMIDs used here directly support the "subepithelial collagen band" concept; please confirm in review whether the intended PMID was different. Signed-off-by: dragon-ai-agent
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Claude finished @dragon-ai-agent's task in 3m 15s —— View job PR Review: NTR collagen band (UBERON:1200005)Review checklist:
SummaryThe term is well-structured overall. The parent
The PR author correctly identified that PMID:25216277 (cited in the original issue) is the paper "Transoral palate-sparing nasopharyngectomy with the Flex® System: preclinical study" — entirely unrelated to collagen layers. This call was right. Issues🟡 IMPORTANT: Two synonyms have no supporting reference These were sourced only from PMID:25216277 in the original NTR. Since that PMID is wrong, these synonyms are currently unsupported. Options:
Leaving synonyms with Suggestions (non-blocking)🔵 SUGGESTION: Consider adding a The definition states the collagen band forms "a distinct layer beneath an epithelium", but there is no logical axiom encoding this positional constraint. Adding e.g. 🔵 SUGGESTION: Note pathological context All cited references describe this band in the context of collagenous gastritis/colitis — a disease phenotype. A brief comment clarifying that the term denotes a pathological structure would help curators and downstream users. Merge recommendationRequest changes due to the unsupported synonyms. Once @aleixpuigb confirms the correct PMID (or the two synonyms are removed pending clarification), this can be approved. |
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Two synonyms lack supporting references ("subepithelial collagen layer" and "superficial subepithelial collagen layer" both have empty xrefs after PMID:25216277 was correctly identified as an unrelated nasopharyngectomy paper). These should either be removed or given a valid citation before merging. All other aspects of the term are well-formed: parent UBERON:0011860 is appropriate, PMIDs 19295410 and 37022603 are confirmed relevant, OBO format is correct, and contributor/date metadata is present. Full review details in the PR comment.
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Claude finished @aleixpuigb's task in 2m 52s —— View job PR Review: NTR collagen band (UBERON:1200005) — updatedReview checklist:
The IMPORTANT issue flagged in the previous review has been fully resolved by @aleixpuigb's commit ("Remove wrong synonym and add reference to exact synonym"):
All four remaining synonyms now carry proper PMID citations. No blocking issues remain. PR approved. ✓ |
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PR Review: NTR collagen band (UBERON:1200005) — updated
Review checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A — new term)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
The IMPORTANT issue flagged in the previous review has been fully resolved by @aleixpuigb's commit ("Remove wrong synonym and add reference to exact synonym"):
- ✅ "subepithelial collagen layer" now correctly cites PMID:30486642 (Mosso et al. 2019, Microscopic colitis: a narrative review with clinical approach, Minerva Gastroenterol Dietol), which discusses collagenous colitis and its characteristic subepithelial collagen layer. This is directly relevant.
- ✅ "superficial subepithelial collagen layer" has been removed (it had no valid supporting reference).
All four remaining synonyms now carry proper PMID citations. The term is well-formed overall.
Final term state
synonym: "collagenous band" EXACT [PMID:37022603]
synonym: "subepithelial collagen band" EXACT [PMID:19295410]
synonym: "subepithelial collagen layer" EXACT [PMID:30486642]
synonym: "subepithelial collagenous band" EXACT [PMID:19295410]
No blocking issues remain. Ready to merge.
🤖 Reviewed by @dragon-ai-agent
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Claude finished @aleixpuigb's task in 3m 14s —— View job PR Review: NTR collagen band (UBERON:1200006)Review checklist:
SummaryThe term is well-formed and all previous blocking issues have been resolved. The parent Final term state (from diff): Issues🔵 NOTE: Term ID changed from 1200005 → 1200006 The PR title and description still refer to If @aleixpuigb changed this because another open PR already claimed UBERON:1200005, then UBERON:1200006 is correct as-is. If it was changed in error, the ID could be reverted to 1200005 to keep the sequence clean. Either way, UBERON:1200006 is a valid unused ID and the term will function correctly — this is informational only. Merge recommendationNo blocking issues remain. The synonyms issue from the previous review is fully resolved. Ready to merge. 🤖 Reviewed by @dragon-ai-agent |
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#gogoeditdiff |
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PR Review: NTR collagen band (UBERON:1200006)
Review checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A — new term)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
The term is well-formed. All blocking issues from the previous review are resolved — all four synonyms now carry valid PMID citations. Parent UBERON:0011860 (collection of collagen fibrils) confirmed present and appropriate. Contributor/date/term_tracker metadata all present.
One informational note: the term ID was changed from UBERON:1200005 to UBERON:1200006 (commit 7d40450), but UBERON:1200005 does not appear in master, so the sequence has a gap. Not blocking.
Ready to merge. 🤖 Reviewed by @dragon-ai-agent
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Claude finished @aleixpuigb's task in 4m 7s —— View job PR Review: NTR collagen band / UBERON:9900064Review checklist:
🔴 CRITICAL: Wrong term is now in this PRCommit The current diff against The collagen band term (UBERON:1200006) that was approved by previous reviewers is no longer present in the branch. Action required — choose one:
Assessment of the GCIPL term (UBERON:9900064) now in the diffThe term itself is well-formed and its OBO relationships are logically sound:
No duplicate GCIPL term exists in uberon-edit.obo. 🔵 SUGGESTION: PMIDs 25208547, 22365056, and 28283025 were not programmatically verifiable in this run — please confirm they resolve to papers about the ganglion cell-inner plexiform layer. Merge recommendationChanges requested. The collagen band (UBERON:1200006) that was approved in earlier reviews is now absent from the branch. Resolve by either restoring it (and moving the GCIPL term to a separate PR for #3729) or explicitly scoping the PR to the GCIPL term only. 🤖 Reviewed by @dragon-ai-agent |
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PR Review: NTR collagen band / UBERON:9900064
Review checklist
- Hierarchy and parents are consistent (for term currently in diff)
- Definitions and supporting references look adequate (for term currently in diff)
- Obsolete or replacement handling is safe (N/A)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
🔴 CRITICAL: Wrong term is now in this PR
Commit a949983 ("Add temp ID") by @aleixpuigb completely replaced the collagen band term (UBERON:1200006) with a different term — UBERON:9900064 ganglion cell-inner plexiform layer — which belongs to issue #3729.
The current diff against master now adds only:
[Term]
id: UBERON:9900064
name: ganglion cell-inner plexiform layer
...
property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3729" xsd:anyURI
The collagen band term (UBERON:1200006) that was approved by previous reviewers is no longer present in the branch.
Action required — choose one:
- Revert commit
a949983to restore the collagen band term, and open a separate PR for the GCIPL term (#3729) - Or, if this is intentional: update the PR title/description and acknowledge that collagen band is no longer included, then track it separately
Assessment of the GCIPL term (UBERON:9900064) now in the diff
The term itself is well-formed and its OBO relationships are logically sound:
| Field | Value | Status |
|---|---|---|
| is_a | UBERON:0000481 multi-tissue structure | ✅ exists |
| part_of | UBERON:0003902 retinal neural layer | ✅ exists |
| has_part | UBERON:0001792 ganglionic layer of retina | ✅ exists |
| has_part | UBERON:0001795 inner plexiform layer of retina | ✅ exists |
| dc-contributor | https://orcid.org/0000-0001-6677-8489 | ✅ present |
| dcterms-date | 2026-06-03T00:00:00Z | ✅ present |
| term_tracker_item | issue #3729 | ✅ correct issue |
No duplicate GCIPL term exists in uberon-edit.obo.
🔵 SUGGESTION for GCIPL: PMIDs 25208547, 22365056, and 28283025 could not be programmatically verified in this review — please confirm these resolve to papers about the ganglion cell-inner plexiform layer.
Merge recommendation
🔴 Request changes: the collagen band (UBERON:1200006) approved in earlier review rounds is now missing. This PR should either be restored to add collagen band, or deliberately retitled/re-scoped before merging.
🤖 Reviewed by @dragon-ai-agent
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Claude finished @aleixpuigb's task in 3m 45s —— View job PR Review: NTR collagen band (UBERON:9900064)Review checklist:
SummaryThe collagen band term has been restored after commit Current term state (from diff): Issues🟡 IMPORTANT: Term ID has changed from UBERON:1200006 → UBERON:9900064 Commit The collagen band was reviewed and approved with ID UBERON:1200006 across two prior review rounds. The current ID was briefly associated with a completely different term in this branch's history. Risks:
Recommended fix: Revert the term ID back to What was resolved
Merge recommendation🟡 Request changes: restore term ID to UBERON:1200006 (the previously approved ID) to avoid potential ID collision with issue #3729. Once that one-line change is made, this PR is ready to merge. 🤖 Reviewed by @dragon-ai-agent |
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PR Review: NTR collagen band
Review checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A — new term)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Summary
The collagen band term has been restored after commit a949983 incorrectly replaced it with the ganglion cell-inner plexiform layer term. The term content is now correct — name, definition, all four synonyms with proper PMID citations, and metadata are all well-formed. The parent UBERON:0011860 (collection of collagen fibrils) is confirmed present and is the correct genus.
Current term state:
[Term]
id: UBERON:9900064
name: collagen band
def: "A band-shaped collection of collagen fibrils forming a distinct layer beneath an epithelium." [PMID:19295410, PMID:37022603]
synonym: "collagenous band" EXACT [PMID:37022603]
synonym: "subepithelial collagen band" EXACT [PMID:19295410]
synonym: "subepithelial collagen layer" EXACT [PMID:30486642]
synonym: "subepithelial collagenous band" EXACT [PMID:19295410]
is_a: UBERON:0011860 ! collection of collagen fibrils
...
Issues
🟡 IMPORTANT: Term ID has changed from UBERON:1200006 → UBERON:9900064
Commit d9cca9d ("Correct term") restored the collagen band name/content, but retained the ID UBERON:9900064 that was introduced by commit a949983 for the wrong term (ganglion cell-inner plexiform layer, issue #3729).
The collagen band was reviewed and approved with ID UBERON:1200006 across two prior review rounds. The current ID was previously — even if briefly — associated with a completely different term in this branch's history.
Risks:
- If a separate PR is opened for issue #3729 (GCIPL term) and the author uses UBERON:9900064 as the temp ID (as was done in commit a949983), there will be a collision.
- The previously approved and reviewed ID (UBERON:1200006) is cleaner and avoids this ambiguity.
Recommended fix: Revert the term ID back to . Fix this →
What was resolved
The blocking issue from the previous review (wrong term in the PR) has been fixed — the ganglion cell-inner plexiform layer term is no longer in the diff. The synonym citation issue from earlier rounds is also fully resolved.
Merge recommendation
🟡 Request changes: restore term ID to UBERON:1200006 (the previously approved ID for collagen band) to avoid ID confusion with issue #3729. Once that one-line change is made, this PR is ready to merge.
🤖 Reviewed by @dragon-ai-agent
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PR Review: NTR collagen band
Review checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A — new term)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Summary
The collagen band term has been restored after commit a949983 incorrectly replaced it with the ganglion cell-inner plexiform layer term. The term content is now correct — name, definition, all four synonyms with proper PMID citations, and metadata are all well-formed. The parent UBERON:0011860 (collection of collagen fibrils) is confirmed present and is the correct genus.
Current term state:
[Term]
id: UBERON:9900064
name: collagen band
def: "A band-shaped collection of collagen fibrils forming a distinct layer beneath an epithelium." [PMID:19295410, PMID:37022603]
synonym: "collagenous band" EXACT [PMID:37022603]
synonym: "subepithelial collagen band" EXACT [PMID:19295410]
synonym: "subepithelial collagen layer" EXACT [PMID:30486642]
synonym: "subepithelial collagenous band" EXACT [PMID:19295410]
is_a: UBERON:0011860 ! collection of collagen fibrils
...
Issues
🟡 IMPORTANT: Term ID has changed from UBERON:1200006 → UBERON:9900064
Commit d9cca9d ("Correct term") restored the collagen band name/content but retained the ID UBERON:9900064 that was introduced by commit a949983 for the wrong term (ganglion cell-inner plexiform layer, issue #3729).
The collagen band was reviewed and approved with ID UBERON:1200006 across two prior review rounds. The current ID was previously — even if briefly — associated with a completely different term in this branch's history.
Risks:
- If a separate PR is opened for issue #3729 (GCIPL term) and the author uses UBERON:9900064 as the temp ID (as was done in commit a949983), there will be an ID collision.
- The previously approved and reviewed ID (UBERON:1200006) is cleaner and avoids this ambiguity.
Recommended fix: Revert the term ID back to UBERON:1200006. Fix this →
What was resolved
The blocking issue from the previous review (wrong term in the PR) has been fixed — the ganglion cell-inner plexiform layer term is no longer in the diff. The synonym citation issue from earlier rounds is also fully resolved.
Merge recommendation
🟡 Request changes: restore term ID to UBERON:1200006 (the previously approved ID for collagen band) to avoid potential ID collision with issue #3729. Once that one-line change is made, this PR is ready to merge.
🤖 Reviewed by @dragon-ai-agent
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@ai4c-agent the changes with the ID were done intentionally, and they will not clash. The initial ID should not have been allowed, as agents should add terms in a temp ID range (as it is now). Once we merge the term, it will refactor the ID to the next allowed one. |
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Claude finished @aleixpuigb's task in 1m 35s —— View job PR Review: NTR collagen band (UBERON:9900064)Review checklist:
SummaryAll previous blocking issues have been resolved. The term is well-formed and approved. Final term state: Notes
PR approved. Ready to merge. ✓ |
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PR Review: NTR collagen band (UBERON:9900064)
Review checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe (N/A — new term)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Summary
All previous blocking issues have been resolved. The term is well-formed and ready to merge.
Final term state:
[Term]
id: UBERON:9900064
name: collagen band
def: "A band-shaped collection of collagen fibrils forming a distinct layer beneath an epithelium." [PMID:19295410, PMID:37022603]
synonym: "collagenous band" EXACT [PMID:37022603]
synonym: "subepithelial collagen band" EXACT [PMID:19295410]
synonym: "subepithelial collagen layer" EXACT [PMID:30486642]
synonym: "subepithelial collagenous band" EXACT [PMID:19295410]
is_a: UBERON:0011860 ! collection of collagen fibrils
relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-Barbé
property_value: dcterms-date "2026-06-03T00:00:00Z" xsd:dateTime
property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3727" xsd:anyURI
created_by: dragon-ai-agent
Notes
- ✅ Term ID UBERON:9900064 is correctly in the temp ID range (UBERON:99xxxxx) per project policy, as clarified by @aleixpuigb. The ID will be refactored to a permanent one after merge.
- ✅ Parent UBERON:0011860 (collection of collagen fibrils) confirmed present and is the appropriate genus.
- ✅ All four synonyms carry valid PMID citations — the synonym citation issues from earlier review rounds are fully resolved.
- ✅ Contributor/date/term_tracker metadata all present and well-formed.
PR approved. Ready to merge. ✓
🤖 Reviewed by @dragon-ai-agent
3 participants
Summary
Adds new term collagen band (UBERON:1200005) as requested in #3727.
Term details
⚠ Note on PMIDs
The issue cited PMID:25216277 as both definition source and synonym source for "subepithelial collagen layer" / "superficial subepithelial collagen layer". However that PMID resolves to a paper on transoral palate-sparing nasopharyngectomy with the Flex System, which is unrelated to subepithelial collagen layers. I therefore used PMID:19295410 (Leung et al. 2009, Collagenous gastritis: histopathologic features and association with other gastrointestinal diseases) and PMID:37022603 (a 2023 scoping review on collagenous gastritis) — both of which explicitly describe the "subepithelial collagen band" concept.
Synonyms whose only citation was PMID:25216277 have been left without an xref pending clarification. Please confirm the correct PMID in review.
Closes #3727
🤖 Generated by @dragon-ai-agent