Add HRA fallopian tube NTR template (58 new terms)

[zhengj2007]

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

[ai4c-agent]

Claude finished @zhengj2007's task in 4m 30s —— View job

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PR Review: Add HRA fallopian tube NTR template (58 new terms)

Review 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

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Summary

This 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.

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🔴 CRITICAL — Must fix before merge

1. UNRESOLVABLE: placeholders in 7 template cells will break the ROBOT build

Six new terms have UNRESOLVABLE:intramural_segment_of_fallopian_tube in their part_of column, and one term (UBERON:8930065) has UNRESOLVABLE:plica of Fallopian tube intramural segment in both its is_a and part_of columns. UNRESOLVABLE: is not a declared OBO prefix, so ROBOT will either error or silently write broken IRIs.

Since intramural segment of fallopian tube (UBERON:8930050) is created in this same PR, all UNRESOLVABLE:intramural_segment_of_fallopian_tube entries should be replaced with UBERON:8930050.

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.

Fix this →

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.

Fix this →

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🟡 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 LABEL is lamina propria Fallopian tube ampulla — missing the word "of". Should be lamina 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-case fallopian matches the existing UBERON terms for this structure.

Fix this →

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 be part_of UBERON:8930050 (intramural segment).
• UBERON:8930087 (serosa of fallopian tube intramural segment): same issue, part_of UBERON:0036441. Should be part_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.

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🔵 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 ampulla definition xref
• PMID:42123609 and PMID:42088488 — mucosa of intramural part of fallopian tube definition 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.

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Positive aspects

• The 7 UNRESOLVABLE entries were properly flagged in errors.tsv and candidates.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.tsv with 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.

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Recommendation: REQUEST CHANGES — The UNRESOLVABLE: entries (#1–2) are build-blocking; items #3–7 should also be resolved before merge.

[ai4c-agent]

CRITICAL — 2 blocking issues:

1. 7 UNRESOLVABLE: entries in hra-fallopian-tube.template.tsv — UBERON:8930044, 8930054, 8930065 (×2), 8930074, 8930083, 8930093, 8930098 reference UNRESOLVABLE:intramural_segment_of_fallopian_tube or UNRESOLVABLE:plica of Fallopian tube intramural segment in their is_a/part_of columns. UNRESOLVABLE: is not a declared OBO prefix and will break ROBOT template processing. Since intramural segment of fallopian tube is UBERON:8930050 (added in this same PR), all such entries should be replaced with UBERON:8930050. For UBERON:8930065 the is_a should be UBERON:0000344 (mucosa) and part_of should be UBERON:8930050.

2. UBERON:8930048 and UBERON:8930079 have blank part_of — inner/outer muscle layers of the intramural segment need part_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 specific UBERON:0012368/0012369 used 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 of UBERON:8930050 (intramural segment).
• Plica terms for ampulla/infundibulum use is_a epithelial fold while isthmus/intramural use oviduct mucosal fold — should be uniform.

Full details in the inline review comment.