Add HRA intestine/liver/skin NTR template (4 new terms)#3716
Add HRA intestine/liver/skin NTR template (4 new terms)#3716zhengj2007 wants to merge 7 commits into
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Generated via bulk_ntr_workflow from source_data/intestine-liver-skin.csv (5 input rows from large-intestine, liver, and skin tables): - 4 new UBERON terms (UBERON:8930100-8930102, UBERON:8930104): - free taenia coli (UBERON:8930100) - mesocolic taenia coli (UBERON:8930101) - omental taenia coli (UBERON:8930102) - connective tissue sheath (UBERON:8930104) - of hair follicle - 1 row excluded as out-of-scope: 'Liver immune resident component' (functional immune-cell collective; belongs in CL, not UBERON) Name corrections applied: 'free coli' -> 'free taenia coli' etc. (source ASCTB labels were incomplete; full anatomical nomenclature used). Signed-off-by: dragon-ai-agent <dragon-ai-agent@users.noreply.github.com>
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Claude finished @zhengj2007's task in 5m 13s —— View job PR ReviewReview checklist:
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SummaryThis PR adds 4 new UBERON terms for intestine/skin anatomy via ROBOT template, generated through the bulk NTR workflow. The scope decisions are well-reasoned (liver immune component correctly excluded as CL, not UBERON). However there are several issues that need to be fixed before merge. 🔴 CRITICAL: Template not registered in ODK YAML
Per the bulk NTR workflow docs (Stage 5), the registration script must be run: cd bulk_ntr_workflow
uv run scripts/register_templates.py --name hra-intestine-liver-skinThis should add an entry like: - filename: hra_intestine_liver_skin.owl
use_template: true
templates:
- hra-intestine-liver-skin.template.tsvto 🟡 IMPORTANT: Incorrect
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REQUEST CHANGES on PR #3716 (Add HRA intestine/liver/skin NTR template).
🔴 CRITICAL: Template hra-intestine-liver-skin.template.tsv is not registered in src/ontology/uberon-odk.yaml — without this the 4 new terms will never be compiled into the ontology build. Stage 5 (register_templates.py) was not run.
🟡 IMPORTANT:
- Taenia coli terms (8930100–8930102) use
is_a: UBERON:0004923+part_of: UBERON:0012419. The three named bands are subtypes of taenia coli (matching FMA's model of FMA:15041 and its subclasses), so the correct axioms areis_a: UBERON:0012419+part_of: UBERON:0011198(muscle layer of large intestine). - Duplicate non-standard
isBN:978-1496398949prefix (typo for ISBN) appears in all three taenia coli def_xrefs — must be removed. - UBERON:8930104 label
connective tissue sheathis too generic; should beconnective tissue sheath of hair follicle.
See detailed review in the Claude comment for fix suggestions.
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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. |
Generate and serialize component in OWL Functional Syntax from template. @dragon-ai-agent
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Claude finished @zhengj2007's task in 5m 36s —— View job Re-review of PR #3716 (after latest push)
Review checklist:
SummaryGood progress since the last review — three of the four previously-flagged issues in
However, new commit 🔴 CRITICAL: Template still not registered in
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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 (commit 9e0bb28).
- Hierarchy and parents are consistent (for the template rows themselves)
- 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
Good progress: the previously flagged is_a/part_of inversion for the three taenia coli terms, the duplicate isBN: typo, and the overly generic "connective tissue sheath" label are all now fixed in src/templates/hra-intestine-liver-skin.template.tsv.
Two blockers remain/were introduced:
🔴 CRITICAL: src/ontology/uberon-odk.yaml still does not register hra-intestine-liver-skin.template.tsv under components.products (only hra_skeleton.owl is present). Without this the 4 new terms will never be compiled into the build.
🔴 CRITICAL: The newly added src/templates/hra-intestine-liver-skin.owl (commit 9e0bb28) is malformed OWL functional syntax — it declares BFO:0000050 (part_of) as a DataProperty instead of ObjectProperty, declares UBERON classes UBERON:0002073 and UBERON:0011198 as Datatypes, and uses DataSomeValuesFrom instead of ObjectSomeValuesFrom in the SubClassOf axioms. It's also in the wrong location — checked-in template-generated components belong under src/ontology/components/ (see hra_skeleton.owl), not src/templates/. This file should be deleted; once the template is registered in uberon-odk.yaml, the ODK build will generate the correct component automatically.
See full details in the PR comment.
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Claude finished @zhengj2007's task in 2m 9s —— View job Re-review of PR #3716 (after commit 67e5830)Tasks:
Review checklist:
SummaryCommit However, the two structural blockers from the last review are still unresolved: 🔴 CRITICAL: Template still not registered in
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Re-review of PR #3716 (after commit 67e5830)
- Hierarchy and parents are consistent (template content)
- 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
Commit 67e5830 fixes the OWL functional-syntax errors flagged previously (ObjectProperty/Class/ObjectSomeValuesFrom now used correctly). Template content (is_a/part_of modeling, isBN typo, label fix) remains correct.
Two blockers remain:
🔴 CRITICAL: src/ontology/uberon-odk.yaml still does not register hra-intestine-liver-skin.template.tsv under components.products (only hra_skeleton.owl is present), and src/ontology/Makefile has no corresponding target. Without this the 4 new terms will never be compiled into the ontology build.
🔴 CRITICAL: src/templates/hra-intestine-liver-skin.owl remains a hand-authored stand-in committed in the wrong location (should be src/ontology/components/), lacking the standard ROBOT versioned-IRI/owl:versionInfo header, and unreferenced by the build. Recommend deleting it — once registration above is done, the ODK build will generate the correct file automatically.
See full details in the PR comment.
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Claude finished @dosumis's task in 1m 50s —— View job Re-review of PR #3716 (after commit b76761d)Tasks:
Review checklist:
SummaryCommit 🔴 CRITICAL: Template still not registered in
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REQUEST CHANGES on PR #3716 (Add HRA intestine/liver/skin NTR template).
No changes since the last review address the two blockers:
🔴 CRITICAL: hra-intestine-liver-skin.template.tsv is still not registered in src/ontology/uberon-odk.yaml (components.products) or src/ontology/Makefile — the 4 new terms will not be compiled into the ontology build.
🔴 CRITICAL: src/templates/hra-intestine-liver-skin.owl remains a hand-authored file in the wrong location (should be a ROBOT-generated artifact under src/ontology/components/), lacking the standard versioned-IRI/owl:versionInfo header. Recommend deleting it — registering the template will make the ODK build generate the correct file automatically.
Template content itself (is_a/part_of modeling, isBN typo, label fix) remains correct since the previous review.
See detailed review in the Claude comment for fix suggestions.
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please merge src/templates/hra-intestine-liver-skin.owl to src/ontology/uberon-edit.obo and then remove src/templates/hra-intestine-liver-skin.owl |
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🤖 Working on it... Follow along: View workflow run |
Merges the 4 new HRA terms (UBERON:8930100 free taenia coli, UBERON:8930101 mesocolic taenia coli, UBERON:8930102 omental taenia coli, UBERON:8930104 connective tissue sheath of hair follicle) from the ROBOT-generated template into the main edit file, and removes the now-redundant src/templates/hra-intestine-liver-skin.owl. Requested by @zhengj2007 in PR #3716. Signed-off-by: @dragon-ai-agent --- 🤖 **Generated by @dragon-ai-agent** - Model: `claude-opus-4-7` - Agent harness: claude-code - Triggered by: @zhengj2007 - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/28838034623)
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Merged What I did
Terms merged
All 4 stanzas carry The diff on 🤖 Generated by @dragon-ai-agent
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Claude finished @dragon-ai-agent's task in 9m 34s —— View job Re-review of PR #3716 (after commit e29097d)Tasks:
Review checklist:
SummaryCommit
This is a reasonable resolution given the small number of terms (4) — it matches the standard 🔵 SUGGESTION: Contributor/date metadata uses a non-standard propertyThe 4 new stanzas use: The rest of the file overwhelmingly uses 🔵 SUGGESTION: Orphaned template files (carried over)
What was done well
Merge recommendationAPPROVE — only non-blocking suggestions remain. |
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Re-review of PR #3716 (after commit e29097d)
Both previously-flagged CRITICAL blockers are now resolved: commit e29097d converted the 4 term stanzas directly into src/ontology/uberon-edit.obo (via the standard obo-checkout.pl/obo-checkin.pl workflow) rather than requiring ODK template registration, and deleted the malformed hand-authored src/templates/hra-intestine-liver-skin.owl. Verified the diff contains exactly the 4 expected [Term] stanzas (UBERON:8930100, 8930101, 8930102, 8930104), parent terms (taenia coli, muscle layer of large intestine, connective tissue, hair follicle) are consistent, and the terms/ scratch directory is clean.
Only non-blocking suggestions remain (see PR comment for details):
- 🔵 Contributor/date metadata on the new terms uses
property_value: terms:contributor/terms:daterather than the repo's dominantrelationship: dc-contributor ... ! <Name>/dcterms-dateconvention — metadata-only, doesn't affect the build. - 🔵 The now-orphaned
src/templates/hra-intestine-liver-skin*.tsvtemplate files remain unregistered in the repo; worth a note or cleanup to avoid future duplicate-term confusion.
Full review details posted in the PR comment.
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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Claude finished @dosumis's task in 2m 12s —— View job Re-review of PR #3716 (after commit 8c51771, requested by @dosumis)Tasks:
Review checklist:
SummaryCommit
This addresses the "orphaned report files under 🔵 SUGGESTION (carried over, still open, non-blocking)
What was done well
Merge recommendationAPPROVE — only non-blocking suggestions remain, none of which affect correctness or the build. |
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Reports relocated. Route: manual hand-edit (4 terms, <20). PMIDs verified real & on-topic. TODO: convert template rows → OBO stanzas in Automated update (@cellsemantic / dragon-ai-agent, for @dosumis). Reports were relocated out of |
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Re-review of PR #3716 (after commit 8c51771)
- 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
Commit 8c51771 is a pure rename: it relocates the report artifacts from src/templates/hra-intestine-liver-skin-reports/ to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/, matching the canonical layout. No content changed, and nothing in uberon-odk.yaml/Makefile referenced the old path, so this is risk-free.
The 4 term stanzas in src/ontology/uberon-edit.obo (UBERON:8930100, 8930101, 8930102, 8930104) remain unchanged and correct — is_a/part_of modeling, definitions, and metadata all check out as in the prior approved review.
Only non-blocking suggestions remain (carried over): the isBN: typo in provenance-only files, the now-orphaned unregistered .template.tsv files in src/templates/, and the terms:contributor/terms:date property_value convention differing from the repo's dominant dc-contributor/dcterms-date style.
APPROVE — no blocking issues.
4 participants
Generated via bulk_ntr_workflow from source_data/intestine-liver-skin.csv (5 input rows from large-intestine, liver, and skin tables):
Name corrections applied: 'free coli' -> 'free taenia coli' etc. (source ASCTB labels were incomplete; full anatomical nomenclature used).