Add HRA fallopian tube NTR template (58 new terms)#3715
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Generated via bulk_ntr_workflow from source_data/fallopian_tube.csv (63 input rows): - 58 new UBERON terms (UBERON:8930037-8930099, leaf template) - 3 confirmed existing matches excluded (mucosa of infundibulum, muscle layer of oviduct infundibulum, serosa of fallopian tube infundibulum) - 3 terms routed to manual_curation - 1 row dropped: 'middle muscle layer of fallopian tube infundibulum' (anatomically questionable - standard anatomy describes only 2 muscle layers) Includes new intramural segment of fallopian tube term + 6 subdivisions (basement membrane, lamina propria, mucosa, nerve, vasculature, wall) that match the structural pattern of existing segments (ampulla, isthmus, infundibulum, fimbria). Outstanding curator follow-ups (see reports/): - 3 manual_curation entries (e.g. serous membrane lining of mesosalpinx redundant with mesosalpinx itself) - Multiple 'middle muscle layer' terms (ampulla, isthmus, intramural) flagged - source ASCTB three-layer model may need reconciliation with standard two-layer anatomy - 2 possible OLS4 matches for curator decision Signed-off-by: dragon-ai-agent <dragon-ai-agent@users.noreply.github.com>
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Claude finished @zhengj2007's task in 4m 30s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms)Review Checklist:
SummaryThis PR adds 58 new UBERON terms for fallopian tube structures via the bulk NTR workflow. The overall structure is sound and the definitions are well-sourced. However, there are 2 critical blocking issues that will cause ROBOT template processing failures, plus several important inconsistencies to address before merge. 🔴 CRITICAL — Must fix before merge1.
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| Term ID | Label | Column | Fix |
|---|---|---|---|
| UBERON:8930044 | fluid of fallopian tube intramural segment | part_of |
UBERON:8930050 |
| UBERON:8930054 | lamina propria of Fallopian tube intramural segment | part_of |
UBERON:8930050 |
| UBERON:8930065 | mucosa of intramural part of fallopian tube | is_a |
UBERON:0000344 (mucosa) |
| UBERON:8930065 | mucosa of intramural part of fallopian tube | part_of |
UBERON:8930050 |
| UBERON:8930074 | nerve of fallopian tube intramural segment | part_of |
UBERON:8930050 |
| UBERON:8930083 | plica of fallopian tube intramural segment | part_of |
UBERON:8930050 |
| UBERON:8930093 | vasculature of Fallopian tube intramural segment | part_of |
UBERON:8930050 |
| UBERON:8930098 | wall of fallopian tube intramural segment | part_of |
UBERON:8930050 |
Note for UBERON:8930065: the ASCTB source confused "plica" (fold) with "mucosa" (epithelial layer). The is_a should be UBERON:0000344 (mucosa), not the plica term — which is confirmed by name_corrections.tsv.
2. Inner/outer muscle layers of intramural segment missing part_of
UBERON:8930048 (inner muscle layer of fallopian tube intramural segment) and UBERON:8930079 (outer muscle layer of fallopian tube intramural segment) have blank part_of columns. Both should have part_of UBERON:8930050.
🟡 IMPORTANT — Should fix before merge
3. Middle muscle layer terms retained despite being anatomically questionable
The PR description notes that middle muscle layer of fallopian tube infundibulum was dropped as "anatomically questionable — standard anatomy describes only 2 muscle layers." Yet the equivalent terms for ampulla (UBERON:8930058), intramural segment (UBERON:8930060), and isthmus (UBERON:8930061) are still included. The manual_curation.tsv documents that standard histological literature (including PMID:2409745, cited in the definitions themselves) consistently describes only two layers (inner circular, outer longitudinal). No independent reference for a middle layer was found. Either all "middle muscle layer" terms should be dropped, or the literature supporting a third layer needs to be cited explicitly.
4. Inconsistent is_a for infundibulum inner/outer muscle sub-layers
The ampulla terms correctly classify the inner layer as is_a UBERON:0012368 (circular muscle layer of muscular coat) and outer as is_a UBERON:0012369 (longitudinal muscle layer of muscular coat). The infundibulum equivalents (UBERON:8930047, UBERON:8930078) use the far more generic is_a UBERON:0004923 (organ component layer). These should use the same genus as the ampulla terms for logical consistency.
5. Naming errors and inconsistent capitalisation of "Fallopian"
- UBERON:8930051
LABELislamina propria Fallopian tube ampulla— missing the word "of". Should belamina propria of fallopian tube ampulla. - Several terms capitalise "Fallopian" (e.g.
vasculature of Fallopian tube ampulla,lamina propria of Fallopian tube fimbria) while others use lower-case. All should follow the same convention — lower-casefallopianmatches the existing UBERON terms for this structure.
6. Incorrect part_of for muscle layer and serosa of intramural segment
- UBERON:8930069 (
muscle layer of oviduct intramural segment):part_of UBERON:0036441(general "wall of fallopian tube"). Should bepart_of UBERON:8930050(intramural segment). - UBERON:8930087 (
serosa of fallopian tube intramural segment): same issue,part_of UBERON:0036441. Should bepart_of UBERON:8930050.
7. Inconsistent is_a for plica terms
plica of fallopian tube ampulla (8930081) and plica of fallopian tube infundibulum (8930082) use is_a UBERON:0005157 (epithelial fold), while the isthmus (8930084) and intramural (8930083) plica terms use the more specific is_a UBERON:0018343 (oviduct mucosal fold). All four should use UBERON:0018343 for consistency and specificity.
🔵 SUGGESTIONS — Optional improvements
8. Anatomical concern: serosa of intramural segment
The intramural segment lies within the myometrium; serosal (peritoneal) covering would be absent or vestigial there. It would be worth adding a comment to UBERON:8930087 noting this caveat, or citing a reference that explicitly describes the serosa in this region.
9. Verify high-numbered PMIDs
The following PMIDs are likely from 2025 and could not be confirmed in this review:
PMID:42032991—mucosa of fallopian tube ampulladefinition xrefPMID:42123609andPMID:42088488—mucosa of intramural part of fallopian tubedefinition xrefs
These should be verified to ensure they are real, accessible publications and that the cited content actually supports the definitions given.
10. Terminology mixing: "oviduct" vs "fallopian tube"
Several term labels use "oviduct" (muscle layer of oviduct ampulla, muscle layer of oviduct isthmus, muscle layer of oviduct intramural segment) while the majority use "fallopian tube". UBERON:0006642 itself carries synonym: "muscle layer of fallopian tube", so a consistent preference for "fallopian tube" in new term labels would be cleaner.
Positive aspects
- The 7
UNRESOLVABLEentries were properly flagged inerrors.tsvandcandidates.tsv— good workflow transparency. - Hierarchical coverage of all four tube segments (ampulla, isthmus, infundibulum, fimbria) plus the new intramural segment is systematic.
- The decision to exclude "serous membrane lining of mesosalpinx" and route it to
manual_curation.tsvwith a clear rationale is good practice. - Parent term choices for most terms (UBERON:0000344, 0005769, 0002049, 0001021, etc.) are anatomically sound.
- ORCID contributor and HRA subset annotations are correctly applied throughout.
Recommendation: REQUEST CHANGES — The UNRESOLVABLE: entries (#1–2) are build-blocking; items #3–7 should also be resolved before merge.
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CRITICAL — 2 blocking issues:
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7
UNRESOLVABLE:entries inhra-fallopian-tube.template.tsv— UBERON:8930044, 8930054, 8930065 (×2), 8930074, 8930083, 8930093, 8930098 referenceUNRESOLVABLE:intramural_segment_of_fallopian_tubeorUNRESOLVABLE:plica of Fallopian tube intramural segmentin theiris_a/part_ofcolumns.UNRESOLVABLE:is not a declared OBO prefix and will break ROBOT template processing. Sinceintramural segment of fallopian tubeis UBERON:8930050 (added in this same PR), all such entries should be replaced withUBERON:8930050. For UBERON:8930065 theis_ashould beUBERON:0000344(mucosa) andpart_ofshould beUBERON:8930050. -
UBERON:8930048 and UBERON:8930079 have blank
part_of— inner/outer muscle layers of the intramural segment needpart_of UBERON:8930050.
IMPORTANT:
- Middle muscle layer terms (8930058, 8930060, 8930061) are included despite the PR itself flagging the three-layer ASCTB model as anatomically questionable and dropping the infundibulum version — should either all be dropped or require explicit literature support for a middle layer.
- Infundibulum inner/outer muscle layers use
is_a UBERON:0004923(generic organ component layer) instead of the more specificUBERON:0012368/0012369used for the ampulla equivalents. - UBERON:8930051 label is "lamina propria Fallopian tube ampulla" (missing "of").
- Inconsistent capitalisation: ~10 terms use "Fallopian" vs the majority using "fallopian".
- UBERON:8930069 and 8930087 have
part_of UBERON:0036441(general wall of fallopian tube) instead ofUBERON:8930050(intramural segment). - Plica terms for ampulla/infundibulum use
is_aepithelial fold while isthmus/intramural use oviduct mucosal fold — should be uniform.
Full details in the inline review comment.
Add hra-fallopian-tube and hra-fallopian-tube-groups templates as components in uberon-odk.yaml, add corresponding imports to uberon-edit.obo, and regenerate the Makefile via `sh run.sh make update_repo`. Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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#gogoeditdiff |
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Claude encountered an error after 0s —— View job I'll analyze this and get back to you. |
PR CI was failing because the catalog had no local-path mapping for the new component IRIs, so the importer was trying to resolve them over the network. Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude encountered an error after 0s —— View job I'll analyze this and get back to you. |
Three fixes to make the new component templates build with ROBOT:
1. Add hra-fallopian-tube-prefixes.owl declaring the annotation
properties (dcterms:date, dcterms:contributor, IAO:0000115,
foaf:depiction, etc.) used by the templates.
2. Override the ODK-generated Makefile rules in uberon.Makefile to
feed the prefixes file and `dcterms:`/`dc:` --prefix flags into
robot template, mirroring the existing hra_skeleton pattern.
3. Resolve UNRESOLVABLE placeholders in the leaf template:
- UNRESOLVABLE:intramural_segment_of_fallopian_tube →
UBERON:8930050 (the new term being introduced in the same batch)
- For "mucosa of intramural part of fallopian tube" (UBERON:8930065),
the placeholder pair was incorrectly the plica label; set
is_a UBERON:0000344 (mucosa) and part_of UBERON:8930050.
Signed-off-by: @dragon-ai-agent
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude encountered an error after 0s —— View job I'll analyze this and get back to you. |
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QC tests pass. Fail is due to lack of Claude credit: 
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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 @zhengj2007's task in 5m 27s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after latest pushReview Checklist:
SummaryI re-reviewed the current state of the branch against the issues raised in the 2026-05-25 review. The 7 🔴 CRITICAL — New issue introduced by latest commit
Commit with no 🟡 IMPORTANT — Still unresolved from prior review
🔵 SUGGESTIONS (unchanged, optional)
Positive aspects
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This PR modifies some logical definitions. See details below:Number of classes with modified logical definitions: 1 gABAergic systemNo changes in inferred subclasses. |
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Re-review after latest push: the 7 UNRESOLVABLE: placeholders from the prior review are correctly resolved, but the most recent commit (6379550) introduces a new critical issue — it edited the template but did not regenerate src/ontology/components/hra_fallopian_tube.owl, so the new is_a axioms for UBERON:8930048/8930060/8930079 are missing from the checked-in artifact. Several IMPORTANT items from the original review also remain unresolved (intramural muscle-layer parentage/is_a still inconsistent with ampulla/isthmus siblings, middle muscle layer terms still unresolved despite new manual_curation.tsv documentation, UBERON:8930069/8930087 part_of still points to the generic wall-of-fallopian-tube term, infundibulum muscle layers still use a generic is_a, naming/capitalisation and plica is_a inconsistencies unchanged). Full details in the PR comment.
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Claude finished @dosumis's task in 3m 6s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after latest pushReview Checklist:
SummaryRe-reviewed the current branch state against the two prior reviews (2026-05-25 and 2026-07-06). The 7 🔴 CRITICAL
🟡 IMPORTANT — still unresolved from prior reviews
All six items above have corresponding inline comments with exact line references and suggested fixes. 🔵 SUGGESTIONS (unchanged, optional)
Positive aspects
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| AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_8930048> "Wikipedia:Fallopian_tube") | ||
| AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_8930048> <http://purl.obolibrary.org/obo/uberon/core#added_by_HRA>) | ||
| AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_8930048> "inner muscle layer of fallopian tube intramural segment") | ||
| SubClassOf(<http://purl.obolibrary.org/obo/UBERON_8930048> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0006660>)) |
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🔴 CRITICAL — still stale after commit 6379550. This checked-in artifact only has SubClassOf(UBERON_8930048 ObjectSomeValuesFrom(part_of UBERON_0006660)). It's missing SubClassOf(UBERON_8930048 UBERON_8930069), even though the template row (hra-fallopian-tube.template.tsv line 14) now has is_a UBERON:8930069. The same gap exists for UBERON:8930060 (line 381) and UBERON:8930079 (line 582). Commit 6379550 edited only the template, not this generated OWL file — the Makefile's timestamp/stamp-file-driven build for this component may not have re-run. Please regenerate hra_fallopian_tube.owl (and check hra_fallopian_tube_groups.owl) via the ROBOT template build and commit the result, otherwise CI/local builds could silently use the stale, incomplete axioms.
| http://purl.obolibrary.org/obo/UBERON_8930045 fluid of fallopian tube isthmus A bodily fluid that is contained within the lumen of the isthmus of the fallopian tube. https://purl.org/ccf/ASCTB-TEMP_fluid-of-fallopian-tube-isthmus UBERON:0006314 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 | ||
| http://purl.obolibrary.org/obo/UBERON_8930046 inner muscle layer of fallopian tube ampulla A circular smooth muscle layer that is part of the muscle coat of the ampulla of the fallopian tube. This layer forms the innermost component of the muscularis and, together with the outer longitudinal layer, generates peristaltic contractions that facilitate oocyte and embryo transport through the ampullar region. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-ampulla|PMID:2409745|PMID:1964529 UBERON:0012368 UBERON:0006642 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930047 inner muscle layer of fallopian tube infundibulum An organ component layer composed primarily of circularly arranged smooth muscle tissue that forms the innermost layer of the muscular coat of the uterine tube infundibulum, contributing to peristaltic contractions that assist in gamete and embryo transport. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-infundibulum|PMID:25866566|PMID:27875265 UBERON:0004923 UBERON:0007182 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube|FMA:18336 | ||
| http://purl.obolibrary.org/obo/UBERON_8930048 inner muscle layer of fallopian tube intramural segment The innermost circular smooth muscle layer of the muscularis of the fallopian tube intramural part, which lies within the uterine wall and contributes to peristaltic contractions that propel the ovum toward the uterus. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-intramural-segment|PMID:25866566 UBERON:8930069 UBERON:0006660 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube |
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🟡 IMPORTANT — partial fix, still unresolved. UBERON:8930048 now has is_a UBERON:8930069 (good), but part_of is still the generic UBERON:0006660 (muscle layer of muscular coat) rather than UBERON:8930050 (intramural segment). This is also true for row 25 (UBERON:8930060) and row 42 (UBERON:8930079). Since UBERON:8930069 itself is part_of UBERON:0036441 (generic "wall of fallopian tube", see row 32) rather than UBERON:8930050, none of these sub-layers are actually linked into the intramural segment's partonomy — they only chain up to the tube as a whole. Suggested fix mirroring the ampulla/isthmus pattern: set part_of to UBERON:8930069 (the segment-specific muscle-layer term) for rows 14, 25, 42, and set row 32's part_of to UBERON:8930050 instead of UBERON:0036441.
| http://purl.obolibrary.org/obo/UBERON_8930065 mucosa of intramural part of fallopian tube A mucosa that is part of the intramural segment of the fallopian tube. The intramural (or interstitial) part of the fallopian tube is the narrowest segment that lies within the myometrium, the muscular wall of the uterus, extending from the uterine cavity to where it opens into the broader isthmus of the tube. https://purl.org/ccf/ASCTB-TEMP_mucosa-of-fallopian-tube-intramural-segment|PMID:42123609|PMID:42088488 UBERON:0000344 UBERON:8930050 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930066 mucosa of fallopian tube isthmus A mucosa that forms the innermost epithelial layer lining the lumen of the isthmus of the fallopian tube, comprising epithelial cells and underlying lamina propria. https://purl.org/ccf/ASCTB-TEMP_mucosa-of-fallopian-tube-isthmus|PMID:25595539|PMID:28413873 UBERON:0000344 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Isthmus_of_uterine_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930067 muscle layer of fallopian tube ampulla A muscular coat consisting of longitudinal outer and circular inner smooth muscle layers that is part of the ampulla of the fallopian tube and is responsible for rhythmic peristaltic contractions. https://purl.org/ccf/ASCTB-TEMP_muscle-layer-of-oviduct-ampulla|PMID:33772852 UBERON:0006660 UBERON:0012648 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/thumb/7/71/Histology_of_ciliated_columnar_epithelium_of_the_fallopian_tube.jpg/250px-Histology_of_ciliated_columnar_epithelium_of_the_fallopian_tube.jpg Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930069 muscle layer of oviduct intramural segment A muscular coat composed of smooth muscle tissue that surrounds the lumen of the intramural segment of the fallopian tube, the portion of the oviduct that traverses the uterine wall between the uterine cavity and the isthmus. https://purl.org/ccf/ASCTB-TEMP_muscle-layer-of-oviduct-intramural-segment|PMID:7004702 UBERON:0006660 UBERON:0036441 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube |
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🟡 IMPORTANT — unchanged from prior review. part_of is UBERON:0036441 (generic "wall of fallopian tube"), not UBERON:8930050 (intramural segment of fallopian tube). Same issue on row 49 (UBERON:8930087, serosa of intramural segment). Both should point to UBERON:8930050.
| http://purl.obolibrary.org/obo/UBERON_8930048 inner muscle layer of fallopian tube intramural segment The innermost circular smooth muscle layer of the muscularis of the fallopian tube intramural part, which lies within the uterine wall and contributes to peristaltic contractions that propel the ovum toward the uterus. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-intramural-segment|PMID:25866566 UBERON:8930069 UBERON:0006660 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930049 inner muscle layer of fallopian tube isthmus A circular smooth muscle layer that forms the innermost component of the muscular coat of the fallopian tube isthmus, contributing to peristaltic contractions that propel the oocyte toward the uterus. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-isthmus UBERON:0012368 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930050 intramural segment of fallopian tube A subdivision of the fallopian tube that lies within the myometrium, the muscular wall of the uterus, connecting the isthmus to the uterine cavity. This is the narrowest and shortest segment of the fallopian tube, measuring approximately 0.7 mm in diameter and 1 cm in length. https://purl.org/ccf/ASCTB-TEMP_intramural-segment-of-fallopian-tube|PMID:2565256|Wikipedia:Fallopian_tube UBERON:0013515 UBERON:0003889 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930051 lamina propria Fallopian tube ampulla A lamina propria that is part of the mucosa of the fallopian tube ampulla, consisting of a thin layer of loose connective tissue underlying the luminal epithelium and containing blood vessels and immune cells. https://doi.org/10.1016/j.celrep.2021.108978|PMID:25994820|PMID:16938110|https://purl.org/ccf/ASCTB-TEMP_lamina-propria-fallopian-tube-ampulla|PMID:7004702 UBERON:0000030 UBERON:0012648 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube |
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🟡 IMPORTANT — unchanged. LABEL is lamina propria Fallopian tube ampulla — missing "of" and capitalised "Fallopian". Should be lamina propria of fallopian tube ampulla. Roughly 9 other rows (e.g. lines 18, 19, 51–55) still capitalise "Fallopian" inconsistently with the lower-case convention used elsewhere (and by existing UBERON terms for this structure).
| http://purl.obolibrary.org/obo/UBERON_8930044 fluid of fallopian tube intramural segment A bodily fluid that is contained within the lumen of the intramural segment of the fallopian tube, providing a medium for the passage of gametes and early embryos through this narrow tubular portion. https://purl.org/ccf/ASCTB-TEMP_fluid-of-fallopian-tube-intramural-segment|PMID:16938110 UBERON:0006314 UBERON:8930050 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 | ||
| http://purl.obolibrary.org/obo/UBERON_8930045 fluid of fallopian tube isthmus A bodily fluid that is contained within the lumen of the isthmus of the fallopian tube. https://purl.org/ccf/ASCTB-TEMP_fluid-of-fallopian-tube-isthmus UBERON:0006314 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 | ||
| http://purl.obolibrary.org/obo/UBERON_8930046 inner muscle layer of fallopian tube ampulla A circular smooth muscle layer that is part of the muscle coat of the ampulla of the fallopian tube. This layer forms the innermost component of the muscularis and, together with the outer longitudinal layer, generates peristaltic contractions that facilitate oocyte and embryo transport through the ampullar region. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-ampulla|PMID:2409745|PMID:1964529 UBERON:0012368 UBERON:0006642 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930047 inner muscle layer of fallopian tube infundibulum An organ component layer composed primarily of circularly arranged smooth muscle tissue that forms the innermost layer of the muscular coat of the uterine tube infundibulum, contributing to peristaltic contractions that assist in gamete and embryo transport. https://purl.org/ccf/ASCTB-TEMP_inner-muscle-layer-of-fallopian-tube-infundibulum|PMID:25866566|PMID:27875265 UBERON:0004923 UBERON:0007182 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube|FMA:18336 |
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🟡 IMPORTANT — unchanged. is_a UBERON:0004923 (generic "organ component layer") for the infundibulum inner muscle layer, and the same on row 41 (outer). The ampulla equivalents (rows 12, 40) correctly use UBERON:0012368/UBERON:0012369 (circular/longitudinal muscle layer of muscular coat) — the infundibulum rows should match for logical consistency.
| http://purl.obolibrary.org/obo/UBERON_8930078 outer muscle layer of fallopian tube infundibulum An organ component layer composed primarily of longitudinally arranged smooth muscle tissue that forms the outermost layer of the muscular coat of the uterine tube infundibulum, contributing to peristaltic contractions that assist in gamete and embryo transport. https://purl.org/ccf/ASCTB-TEMP_outer-muscle-layer-of-fallopian-tube-infundibulum|PMID:25866566|PMID:27875265 UBERON:0004923 UBERON:0007182 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube|FMA:18336 | ||
| http://purl.obolibrary.org/obo/UBERON_8930079 outer muscle layer of fallopian tube intramural segment The outermost longitudinal smooth muscle layer of the muscularis of the fallopian tube intramural part, which lies within the uterine wall and contributes to peristaltic contractions that propel the ovum toward the uterus. https://purl.org/ccf/ASCTB-TEMP_outer-muscle-layer-of-fallopian-tube-intramural-segment|PMID:25866566 UBERON:8930069 UBERON:0006660 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930080 outer muscle layer of fallopian tube isthmus A longitudinal smooth muscle layer that forms the outermost component of the muscular coat of the fallopian tube isthmus, arranged parallel to the long axis of the tube. https://purl.org/ccf/ASCTB-TEMP_outer-muscle-layer-of-fallopian-tube-isthmus UBERON:0012369 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930081 plica of fallopian tube ampulla An epithelial fold that is part of the mucosa of the fallopian tube ampulla, forming an extensive array of complex folds that increase the surface area for ciliated and secretory epithelial cells involved in oocyte transport and fertilization. https://purl.org/ccf/ASCTB-TEMP_plica-of-fallopian-tube-ampulla|PMID:34496720|PMID:33167378 UBERON:0005157 UBERON:0012648 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube |
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🟡 IMPORTANT — unchanged. Row 44 (UBERON:8930081, plica of ampulla) and row 45 (UBERON:8930082, plica of infundibulum) use is_a UBERON:0005157 (epithelial fold), while row 46 (UBERON:8930083, intramural) and row 47 (UBERON:8930084, isthmus) use the more specific UBERON:0018343 (oviduct mucosal fold). Recommend all four use UBERON:0018343 for consistency.
| http://purl.obolibrary.org/obo/UBERON_8930055 lamina propria of Fallopian tube isthmus A lamina propria that is part of the isthmus of the fallopian tube, consisting of a thin layer of loose connective tissue underlying the luminal epithelium. https://doi.org/10.1016/j.celrep.2021.108978|PMID:25994820|PMID:16938110|https://purl.org/ccf/ASCTB-TEMP_lamina-propria-of-fallopian-tube-isthmus UBERON:0000030 UBERON:0016632 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube | ||
| http://purl.obolibrary.org/obo/UBERON_8930056 lymphatic of mesosalpinx A lymphatic vessel that drains lymph from the mesosalpinx, the serous mesenteric fold extending from the fallopian tube to the ovary. https://purl.org/ccf/ASCTB-TEMP_lymphatic-of-mesosalpinx|PMID:29763118 UBERON:0001473 UBERON:0012331 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Mesosalpinx | ||
| http://purl.obolibrary.org/obo/UBERON_8930057 mesothelium of mesosalpinx A mesothelium that forms the epithelial lining of the mesosalpinx, the portion of the broad ligament surrounding the fallopian tube. https://doi.org/10.1016/B978-0-12-801238-3.64401-X|https://purl.org/ccf/ASCTB-TEMP_mesothelium-of-mesosalpinx|PMID:29763118 UBERON:0001136 UBERON:0012331 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Mesosalpinx | ||
| http://purl.obolibrary.org/obo/UBERON_8930058 middle muscle layer of fallopian tube ampulla A smooth muscle layer that is part of the muscle coat of the ampulla of the fallopian tube, situated between the inner circular and outer longitudinal muscle layers. This intermediate layer contributes to the contractile function of the ampulla during gamete and early embryo transport. https://purl.org/ccf/ASCTB-TEMP_middle-muscle-layer-of-fallopian-tube-ampulla|PMID:2409745|PMID:24176284 UBERON:0006660 UBERON:0006642 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Fallopian_tube |
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🟡 IMPORTANT — unchanged. "Middle muscle layer" terms (row 24 UBERON:8930058 ampulla, row 25 UBERON:8930060 intramural, row 26 UBERON:8930061 isthmus) remain, despite manual_curation.tsv now documenting (rows 3–4) that standard histology (PMID:1168021, PMID:2409745, PMID:31613440) describes only two muscularis layers, with no independent literature support found for a third. The PR itself already dropped the equivalent infundibulum term for this reason. Either drop these three terms too, or add explicit literature support/curator sign-off for a three-layer model.
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Re-review after latest push: the 7 UNRESOLVABLE: placeholders are correctly resolved, but the critical stale-artifact issue from the last re-review is still present — src/ontology/components/hra_fallopian_tube.owl was never regenerated after commit 6379550 added is_a UBERON:8930069 to the template rows for UBERON:8930048/8930060/8930079, so the checked-in OWL is missing those axioms. Most of the previously flagged IMPORTANT items (intramural muscle-layer part_of still pointing to generic terms rather than UBERON:8930050, middle muscle layer terms still unresolved despite new manual_curation.tsv literature review, infundibulum muscle layers still using a generic is_a, naming/capitalisation and plica is_a inconsistencies) also remain unaddressed. Full details with exact line references and suggested fixes are in the inline comments and the PR summary comment.
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@dragon-ai-agent Please update src/templates/hra-fallopian-tube.template.tsv as below
After updating the src/templates/hra-fallopian-tube.template.tsv, regenerate src/ontology/components/hra_fallopian_tube.owl |
Updates per @zhengj2007's request (PR #3715): 1. Intramural muscle-layer part_of: set to UBERON:8930069 (segment muscle layer) for the three sub-layers (8930048, 8930079), and set UBERON:8930069's part_of to UBERON:8930050 (intramural segment). 2. UBERON:8930087 (serosa of intramural segment) part_of set to UBERON:8930050. 3. Dropped middle muscle layer terms (UBERON:8930058, 8930060, 8930061) as anatomically unsupported (only inner circular and outer longitudinal are described in standard histology). 4. Infundibulum inner/outer muscle layer is_a changed to UBERON:0012368/UBERON:0012369 respectively, matching ampulla siblings. 5. UBERON:8930051 label fixed: "lamina propria Fallopian tube ampulla" -> "lamina propria of fallopian tube ampulla"; all "Fallopian" in labels lowercased to "fallopian". 6. Plica is_a for ampulla (8930081) and infundibulum (8930082) changed from UBERON:0005157 to UBERON:0018343 (oviduct mucosal fold), matching isthmus/intramural plica terms. 7. UBERON:8930069 and UBERON:8930070 labels: "oviduct" -> "fallopian tube". Regenerated src/ontology/components/hra_fallopian_tube.owl. Signed-off-by: @dragon-ai-agent
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Claude finished @dragon-ai-agent's task in 3m 8s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — verified curator-requested fixes (commit
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| # | Request | Verified |
|---|---|---|
| 1 | part_of UBERON:8930069 for inner/outer intramural muscle sub-layers; part_of UBERON:8930050 for UBERON:8930069 |
✅ UBERON:8930048/8930079 → part_of UBERON:8930069; UBERON:8930069 → part_of UBERON:8930050. Confirmed identical in both template and OWL (SubClassOf(... BFO_0000050 ...) axioms). |
| 2 | part_of UBERON:8930050 for UBERON:8930069 / UBERON:8930087 |
✅ Both now part_of UBERON:8930050 in template and OWL. |
| 3 | Drop middle muscle layer terms (8930058, 8930060, 8930061) | ✅ All three IDs absent from template, OWL, and repo-wide (git grep confirms no dangling references). Row/class counts are consistent: 55 data rows in template = 55 Class declarations in the OWL (58 original − 3 dropped). |
| 4 | Infundibulum inner/outer muscle layers is_a → UBERON:0012368/UBERON:0012369 |
✅ UBERON:8930047 → UBERON:0012368, UBERON:8930078 → UBERON:0012369, matching the ampulla pattern. |
| 5 | Fix "of" + lowercase "fallopian" in labels | ✅ UBERON:8930051 label now lamina propria of fallopian tube ampulla. Confirmed no capitalised "Fallopian" remains anywhere in the LABEL column. |
| 6 | Plica is_a → UBERON:0018343 for ampulla/infundibulum |
✅ UBERON:8930081 and UBERON:8930082 now both use UBERON:0018343, consistent with isthmus/intramural plica terms. |
| 7 | "oviduct" → "fallopian tube" in UBERON:8930069/8930070 labels | ✅ Both now read "muscle layer of fallopian tube intramural segment" / "muscle layer of fallopian tube isthmus". Confirmed no "oviduct" remains in the LABEL column. |
OWL regeneration check: Previously flagged as the blocking issue in the last two reviews — verified this is now fixed. The SubClassOf axioms for UBERON:8930048, 8930069, 8930079, and 8930087 in the committed hra_fallopian_tube.owl exactly match the current template rows (both is_a and part_of/BFO_0000050 axioms), so the artifact is no longer stale.
🔵 Residual observations (non-blocking, optional for a follow-up)
- UBERON:8930048/8930079 now carry both
is_a UBERON:8930069andpart_of UBERON:8930069— i.e. the same term is used as both genus and mereological parent, which loses the circular/longitudinal muscle distinction the ampulla/isthmus siblings preserve viaUBERON:0012368/UBERON:0012369. This wasn't part of the curator's explicit punch list (and a same-day earlier review round had accepted this as "good"), so not blocking, but worth a future look if the reasoner ever needs to distinguish inner vs. outer intramural muscle sub-layers logically. - High-numbered PMIDs (
PMID:42032991,PMID:42123609,PMID:42088488) on the mucosa terms are still worth a final sanity check to confirm they resolve to real, on-topic 2025 publications. - Serosa of intramural segment (UBERON:8930087): still worth a comment noting serosal covering may be vestigial/absent in this region, given the segment lies within the myometrium.
None of these are merge-blocking.
Positive aspects
- All 7 curator-requested changes were implemented correctly and consistently across template + generated OWL.
- Term/class counts line up exactly (55 rows ↔ 55 OWL classes), confirming the drop of the 3 middle-muscle-layer terms didn't leave orphaned references anywhere in
src/. - No stale-artifact regression this time —
hra_fallopian_tube.owlwas properly regenerated alongside the template edit.
gh pr review 3715 --approve issued.
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PR Review: Add HRA fallopian tube NTR template (58 new terms) — verified curator-requested fixes (commit 1ca3f2a)
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
All 7 items from @zhengj2007's punch list are correctly implemented in both src/templates/hra-fallopian-tube.template.tsv and the regenerated src/ontology/components/hra_fallopian_tube.owl:
- part_of UBERON:8930069 for inner/outer intramural muscle sub-layers; part_of UBERON:8930050 for UBERON:8930069 — verified in template and OWL axioms.
- UBERON:8930069 / UBERON:8930087 part_of UBERON:8930050 — verified.
- Middle muscle layer terms (8930058, 8930060, 8930061) dropped — confirmed absent from template, OWL, and repo-wide (no dangling refs). Row/class counts consistent (55 rows = 55 OWL classes = 58 original - 3 dropped).
- Infundibulum inner/outer muscle layers is_a -> UBERON:0012368/UBERON:0012369 — verified.
- Naming/capitalisation fixes (UBERON:8930051 "of", lowercase "fallopian" throughout) — verified, no capitalised "Fallopian" remains in LABEL column.
- Plica is_a -> UBERON:0018343 for ampulla/infundibulum (8930081, 8930082) — verified.
- "oviduct" -> "fallopian tube" in labels for UBERON:8930069/8930070 — verified, no "oviduct" remains in LABEL column.
Critically, the OWL artifact regeneration issue that blocked the prior two reviews is resolved — the SubClassOf axioms in the committed OWL file now match the template exactly.
Non-blocking residual notes: UBERON:8930048/8930079 now use the same term (UBERON:8930069) for both is_a and part_of, losing the circular/longitudinal distinction the ampulla/isthmus siblings have; a few high-numbered PMIDs on mucosa terms are still worth a final sanity check; serosa of the intramural segment (UBERON:8930087) may warrant a comment noting serosal covering could be vestigial there. None of these block merge.
🤖 Generated with Claude Code
Reports are review artifacts, not ODK templates, and should not live under src/templates/. Relocated to bulk_ntr_workflow/outputs/ to match the canonical layout used by the muscular branch (PR #3700). Signed-off-by: dragon-ai-agent
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Reports relocated to To check: CI green after rebase; final review of definitions/parents. Automated update (@cellsemantic / dragon-ai-agent, for @dosumis). Reports were relocated out of |
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Claude finished @dosumis's task in 3m 53s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after report relocation (commit
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| steps: | ||
| - name: Checkout main | ||
| uses: actions/checkout@v6 | ||
| uses: actions/checkout@v4 |
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🟡 IMPORTANT — unintended downgrade of actions/checkout. This PR branch pins actions/checkout@v4, but master (as of commit 651f79c, the release merged into this branch on 97ca8c6) already uses actions/checkout@v6. This looks like a stale merge-conflict resolution that reverted the upgrade rather than an intentional change (this file isn't otherwise related to the fallopian tube NTR work). Suggest restoring actions/checkout@v6 to match master and avoid silently reintroducing an older, unsupported action version into the docs-deploy workflow.
| uses: actions/checkout@v4 | |
| uses: actions/checkout@v6 |
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PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after report relocation (commit 8f9da52)
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression — one issue found
One new, unrelated regression found in this push:
🟡 IMPORTANT — .github/workflows/docs.yml downgrades actions/checkout from v6 (current master) back to v4. This looks like a stale merge-conflict resolution from earlier in the branch history (commit f8777a6), unrelated to the fallopian tube NTR content itself. Inline suggestion posted to restore @v6 to match master.
Everything else verified clean:
- Report relocation (commit 8f9da52) is a pure file move with no content changes and no build-config references to the old path — safe.
- All 7 items from the curator's punch list (commit 1ca3f2a) remain correctly applied in both the template and the regenerated OWL — no regressions, no UNRESOLVABLE placeholders.
- uberon-edit.obo import block is correctly wired.
Recommend fixing the actions/checkout downgrade before merge; the ontology content itself is otherwise ready.
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#gogoeditdiff |
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#gogoeditdiff |
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Claude finished @dosumis's task in 2m 24s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after report relocation + master mergeTodo list:
Checklist:
SummaryRe-verified the branch state, which is now merged with the latest 🟡 IMPORTANT — unresolved regression, flagged in two prior reviews (2026-07-09): Everything else checked clean: the merge of master brought in unrelated repo files ( Recommendation: REQUEST CHANGES — solely for the |
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PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after report relocation + master merge (commits 8f9da52, 9e0e2d0/28f8e76)
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression — one issue persists
Summary
Re-verified the branch state (now merged with the latest master). The ontology content itself remains solid: all 7 items from @zhengj2007's curator punch list (verified and approved at commit 1ca3f2a) are still correctly applied in both src/templates/hra-fallopian-tube.template.tsv and the regenerated src/ontology/components/hra_fallopian_tube.owl — no UNRESOLVABLE: placeholders, intramural muscle-layer parentage chains correctly into UBERON:8930050, middle-muscle-layer terms remain dropped, infundibulum muscle layers use the specific UBERON:0012368/UBERON:0012369, plica is_a is uniformly UBERON:0018343 for ampulla/infundibulum, labels are consistently lower-case "fallopian", and "oviduct" no longer appears in labels.
🟡 IMPORTANT — unresolved regression, flagged in two prior reviews (2026-07-09): .github/workflows/docs.yml still pins actions/checkout@v4, while master (now merged into this branch) uses actions/checkout@v6. This is unrelated to the fallopian tube NTR content and appears to be a stale merge-conflict resolution that has persisted through the last two review rounds. Inline suggestion posted again. I'm not able to fix this myself since GitHub App permissions don't allow edits under .github/workflows/ — this needs a maintainer commit.
Everything else checked clean: the merge of master brought in unrelated repo files (.claude/, CONTRIBUTING.md, issue templates, etc.) with no interaction with the fallopian tube template/OWL content; CI ("Check for modified inferences") passed; no new UNRESOLVABLE: or naming regressions introduced.
Recommendation: REQUEST CHANGES — solely for the actions/checkout downgrade; the ontology content is otherwise ready to merge once that one-line workflow fix lands.
Co-authored-by: ai4c-agent[bot] <242316268+ai4c-agent[bot]@users.noreply.github.com>
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Claude finished @dosumis's task in 2m 34s —— View job PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after
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PR Review: Add HRA fallopian tube NTR template (58 new terms) — re-review after 804df02
Checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Summary
The only outstanding blocker from the prior review — .github/workflows/docs.yml pinning actions/checkout@v4 instead of master's @v6 — was fixed in commit 804df02 (applying the suggested diff). Verified: git diff origin/master...HEAD -- .github/workflows/docs.yml now shows only a trailing-newline difference, no version regression.
Re-verified the full curator punch list directly against the current template and regenerated OWL:
- No
UNRESOLVABLE:placeholders remain insrc/templates/hra-fallopian-tube.template.tsv. - No "oviduct" remains in the LABEL column; no capitalised "Fallopian" in labels (only in
Wikipedia:Fallopian_tubexrefs, which is correct). - Middle-muscle-layer terms (UBERON:8930058/8930060/8930061) remain dropped.
- Infundibulum inner/outer muscle layers (UBERON:8930047/8930078) use the specific
UBERON:0012368/UBERON:0012369. - Intramural muscle sub-layers (UBERON:8930048/8930079) correctly chain
is_a/part_ofintoUBERON:8930069, which itself ispart_of UBERON:8930050(intramural segment); UBERON:8930087 (serosa) is likewisepart_of UBERON:8930050. - Plica terms (UBERON:8930081/8930082) use
UBERON:0018343, consistent with isthmus/intramural siblings. - UBERON:8930051 label correctly reads "lamina propria of fallopian tube ampulla".
- Spot-checked the committed
src/ontology/components/hra_fallopian_tube.owlagainst the template for UBERON:8930048/8930069/8930079/8930087 — axioms match exactly, so the artifact is not stale.
CI: "Check for modified inferences" passed; "CI" was still in progress at review time. "AI Agent GitHub Mentions" shows a failure but this is an unrelated workflow-runner job, not a build/test failure of the ontology content.
Recommendation: APPROVE. All previously identified issues (UNRESOLVABLE placeholders, missing part_of, middle-muscle-layer terms, inconsistent is_a/part_of, naming/capitalisation, plica is_a, oviduct terminology, and the actions/checkout downgrade) are now resolved.
3 participants
Generated via bulk_ntr_workflow from source_data/fallopian_tube.csv (63 input rows):
Includes new intramural segment of fallopian tube term + 6 subdivisions (basement membrane, lamina propria, mucosa, nerve, vasculature, wall) that match the structural pattern of existing segments (ampulla, isthmus, infundibulum, fimbria).
Outstanding curator follow-ups (see reports/):