Add HRA placenta NTR batch outputs and review reports - #3721
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Generated via bulk_ntr_workflow from source_data/placenta.csv. Pipeline completed through Stage 4: - 2 new UBERON leaf terms in final template (endometrial lymphatic vessel, villous mesenchyme) - 0 group terms - 14 confirmed existing matches excluded - 2 possible matches identified (chorionic mesoderm→UBERON:0003265, others) - 0 out-of-scope terms - 0 manual-curation items Resolved final pending row (UBERON_8930179 chorionic mesoderm) by excluding as duplicate of UBERON:0003265 (chorionic mesenchyme). Includes: - Template and groups TSVs in src/templates/ - Detailed review reports: candidates, errors, input, name_corrections - Source data snapshot in bulk_ntr_workflow/source_data/
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Claude finished @zhengj2007's task in 6m 33s —— View job PR Review: Add HRA Placenta NTR Batch OutputsReview checklist:
SummaryThis PR adds two new leaf terms for the HRA placenta batch ( 🟡 IMPORTANT: Undeclared file changesThe PR description lists 7 files, but the actual diff includes 9 files — two unmentioned changes:
These appear unrelated to the HRA placenta NTR work. The Makefile change looks like a legitimate improvement (adds yml metadata support for the biomappings mirror), but the version downgrade in the biomappings snapshot is unexpected. Please confirm these changes are intentional and describe them in the PR body. 🟡 IMPORTANT: Villous mesenchyme — possible duplicate not explicitly resolved
The new term is defined as: "A mesenchyme that is part of a chorionic villus" From a biological standpoint, mesenchyme (embryonic/undifferentiated connective tissue) and stroma (mature supportive tissue framework) are conceptually distinct — so a new term may be warranted. However, the pipeline explicitly flagged this for curator review, and the PR creates the term without documenting the rationale. Please either: (a) Add a comment on the new term explaining why it's distinct, e.g.:
(b) Or, if synonymous, add 🟡 IMPORTANT: PMIDs for villous mesenchyme not verifiableThe two
These are very high-numbered PMIDs (~42 million) that would represent very recent publications. Web search returned no results for either. Please verify these are real, indexed PubMed articles. If they are preprints or not yet indexed, substitute with a confirmed DOI or PMID. By contrast, the PMIDs for
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Requesting changes on this PR. Key issues:
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Undeclared file changes:
src/mappings/biomappings.sssom.tsv(version downgrade 0.5.1-dev→0.5.0-dev, column structure change) andsrc/ontology/uberon.Makefileare modified but not mentioned in the PR description. Please confirm these are intentional. -
Villous mesenchyme possible duplicate unresolved: The pipeline's
candidates.tsvflagsvillous mesenchymeas a possible_match for existingUBERON:8600023 placental villous stroma('A stroma that is part of a chorionic villus'). The PR creates UBERON:8930189 without documenting why it's distinct. Please add a comment or explanation — either justify the new term (mesenchyme vs stroma distinction) or make it a synonym of UBERON:8600023. -
Unverifiable PMIDs: PMID:42146334 and PMID:42048630 for
villous mesenchymecould not be confirmed via web search. Please verify these are indexed in PubMed before merge.
Full review details in the Claude comment on this PR.
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Requesting changes. Key issues:
- Undeclared file changes: src/mappings/biomappings.sssom.tsv (version downgrade 0.5.1-dev to 0.5.0-dev) and src/ontology/uberon.Makefile modified but not mentioned in PR description.
- Villous mesenchyme (UBERON:8930189) flagged as possible duplicate of UBERON:8600023 (placental villous stroma) in the pipeline's own candidates.tsv. New term created without documenting rationale.
- PMIDs for villous mesenchyme (42146334, 42048630) could not be verified via web search.
See full review in the PR comment.
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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. |
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. Route: manual hand-edit (<20). PMIDs verified real (42146334, 42048630, 19001552, 17981324, 17347164). TODO: convert to OBO stanzas. Automated update (@cellsemantic / dragon-ai-agent, for @dosumis). Reports were relocated out of |
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Claude finished @dosumis's task in 4m 44s —— View job PR Review: Add HRA Placenta NTR Batch Outputs (re-review after synchronize)Review checklist:
SummaryThis is a re-review after the branch was updated (commit Two issues from the original review remain unresolved: 🟡 IMPORTANT:
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| ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref | ||
| ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| | ||
| http://purl.obolibrary.org/obo/UBERON_8930180 endometrial lymphatic vessel A lymphatic vessel that is part of the endometrium. Endometrial lymphatic vessels participate in tissue drainage and immune cell trafficking, with lymphangiogenesis occurring during different phases of the menstrual cycle under the regulation of vascular endothelial growth factors. https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel|PMID:19001552|PMID:17981324|PMID:17347164 UBERON:0001473 UBERON:0001295 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Endometrium | ||
| http://purl.obolibrary.org/obo/UBERON_8930189 villous mesenchyme A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers. https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme|PMID:42146334|PMID:42048630 UBERON:0003104 UBERON:0007106 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Chorionic_villi |
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🟡 IMPORTANT (unresolved from prior review): This row creates UBERON:8930189 villous mesenchyme, but bulk_ntr_workflow/outputs/hra-placenta-reports/candidates.tsv (row 16) still flags it as a possible_match for the existing UBERON:8600023 placental villous stroma. Comparing definitions:
UBERON:8600023: "A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast."UBERON:8930189(this row): "A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers."
These are near-duplicate in content, differing mainly in genus (stroma vs. mesenchyme). Per the bulk_ntr_workflow QC checklist ("Review <name>-reports/candidates.tsv — possible_match rows need curator decision"), this needs an explicit curator decision before merge: either (a) add a comment: on the new term explaining the mesenchyme/stroma distinction, or (b) fold villous mesenchyme in as a synonym of UBERON:8600023 instead of minting a new term.
Also note the two def_xref PMIDs (PMID:42146334, PMID:42048630) could not be verified via web search in this review pass (same limitation as the previous review). A recent unsigned PR comment claims they were "verified real," but that claim isn't independently substantiated here — please have a curator confirm these resolve to real, indexed PubMed records before merge.
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Re-review after the branch was synchronized (commit 2305b60). The previously-flagged undeclared file changes (biomappings.sssom.tsv, uberon.Makefile) are resolved — the diff is now cleanly scoped to the 7 declared files.
Two IMPORTANT issues remain unresolved from the original review:
UBERON:8930189 villous mesenchymeis still flagged as apossible_matchfor existingUBERON:8600023 placental villous stromain candidates.tsv, with near-duplicate definitions, and no curator decision (comment or synonym) has been added to resolve it.- The def_xref PMIDs for villous mesenchyme (PMID:42146334, PMID:42048630) still cannot be independently verified. A PR comment claiming they were "verified real" and urging a direct hand-edit into uberon-edit.obo offers no evidence for that claim — recommend independent PMID verification before merge rather than acting on that comment.
Full details in the PR comment and inline comment on src/templates/hra-placenta.template.tsv:4.
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The two def_xref PMIDs for UBERON:8930189 have been confirmed via web search: Please reset two accidentally modified files to match the master branch: Remove empty file: src/templates/hra-placenta-groups.template.tsv Create two new terms based on src/templates/hra-placenta.template.tsv, and add them to src/ontology/uberon-edit.obo. Assign ID: UBERON:8930181 to term "villous mesenchyme", rather than UBERON:8930189. Then add comment to the term UBERON:8930181, "Villous mesenchyme refers to the embryonic connective tissue core of the developing chorionic villus; distinct from placental villous stroma (UBERON:8600023) which denotes the mature stromal compartment." |
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🤖 Working on it... Follow along: View workflow run |
…(villous mesenchyme); revert accidental file changes
- Add two new HRA-requested placenta NTR terms to uberon-edit.obo:
- UBERON:8930180 endometrial lymphatic vessel
- UBERON:8930181 villous mesenchyme (with a distinguishing comment vs.
UBERON:8600023 placental villous stroma; previously staged as 8930189
in the template and reassigned to 8930181 per request).
- Update src/templates/hra-placenta.template.tsv to use UBERON:8930181
for villous mesenchyme (was UBERON:8930189).
- Reset src/mappings/biomappings.sssom.tsv and src/ontology/uberon.Makefile
to master to undo accidental modifications.
- Delete empty src/templates/hra-placenta-groups.template.tsv.
Signed-off-by: @dragon-ai-agent
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🤖 **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/29267642486)
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I've applied the requested changes to this branch (commit Reverted accidental modifications
Cleanup
New terms added to
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Claude finished @zhengj2007's task in 3m 2s —— View job SummaryAll requested changes were already present on this branch (commit
Note on PMID verificationI was not able to independently confirm Nothing else changed by this run — the branch already matched the request. |
4 participants
Generated via bulk_ntr_workflow from source_data/placenta.csv.
Pipeline completed through Stage 4:
Resolved final pending row (UBERON_8930179 chorionic mesoderm) by excluding as duplicate of UBERON:0003265 (chorionic mesenchyme).
Includes: