Add HRA kidney NTR template (2 new terms) - #3717
Conversation
Generated via bulk_ntr_workflow from source_data/kidney.csv: - 2 new UBERON terms (UBERON:8930105-8930106) - kidney lymphatic vessel - epithelium of tip of renal papilla - 0 parent-mapping errors (all source parents were UBERON IDs) - 0 confirmed existing matches, 0 out-of-scope, 0 manual curation - 1 name correction applied: 'Papillary Tip Epithelium' -> 'epithelium of tip of renal papilla' Note: kidney lymphatic vessel includes PMID:24065628; papillary tip epithelium still needs curator-supplied PMID/DOI beyond ASCTB/Wikipedia references. Signed-off-by: dragon-ai-agent <dragon-ai-agent@users.noreply.github.com>
|
Claude finished @zhengj2007's task in 3m 55s —— View job PR Review — Add HRA Kidney NTR Template (2 New Terms)Checklist:
Todo List:
SummaryTwo new terms are proposed for the HRA kidney atlas:
Both IDs fall within the allocated range Issues Found🔴 CRITICAL — Templates not registered in
|
![ai4c-agent[bot]](https://avatars.githubusercontent.com/in/2242960?s=60&v=4){kind=small}
There was a problem hiding this comment.
Two new terms are well-formed and anatomically appropriate, but the PR has one blocker before merge:
🔴 CRITICAL: hra-kidney.template.tsv and hra-kidney-groups.template.tsv are not registered in src/ontology/uberon-odk.yaml. Without entries analogous to the existing hra_skeleton.owl component, the ODK build will never process these templates and the terms will not appear in the generated ontology. Run bulk_ntr_workflow/scripts/register_templates.py --name hra-kidney (or add entries manually) before merging.
🟡 IMPORTANT: epithelium of tip of renal papilla (UBERON:8930106) has only an ASCTB-TEMP placeholder IRI as its def_xref — a real PMID/DOI is required per the NTR workflow QC checklist.
See the full review comment for details and fix links.
|
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. |
|
Please synchronize this branch to base branch. Remove empty file: src/templates/hra-kidney-groups.template.tsv Modify file: src/templates/hra-kidney.template.tsv Add two new terms listed in the src/templates/hra-kidney.template.tsv to src/ontology/uberon-edit.obo |
|
🤖 Working on it... Follow along: View workflow run |
|
🤖 Working on it... Follow along: View workflow run |
…edit.obo
- Merged master into add-hra-kidney-ntr (previous commit).
- Removed empty template file src/templates/hra-kidney-groups.template.tsv.
- Added a `synonym` column (hasRelatedSynonym) to src/templates/hra-kidney.template.tsv
and recorded "papillary tip epithelium" as a related synonym of UBERON:8930106
(per name_corrections: keep source name as synonym).
- Added the two NTR terms declared in the template directly to
src/ontology/uberon-edit.obo so they appear in the core ontology:
- UBERON:8930105 kidney lymphatic vessel
is_a lymphatic vessel; part_of kidney; in_taxon Homo sapiens
def sources: ASCTB-TEMP IRI + PMID:24065628
- UBERON:8930106 epithelium of tip of renal papilla
is_a epithelium; part_of tip of renal papilla; in_taxon Homo sapiens
synonym: "papillary tip epithelium" RELATED; xref Wikipedia:Renal_papilla
Both carry subset added_by_HRA, contributor Jie Zheng (ORCID
0000-0002-2999-0103), dcterms-date 2026-05-26, and term_tracker_item PR #3717.
- Reserialised the edit file with `robot convert -f obo`.
Signed-off-by: @dragon-ai-agent
---
🤖 Generated by @dragon-ai-agent
- Model: claude-opus-4-7
- Agent harness: claude-code
- Triggered by: @zhengj2007
- Run: https://github.com/obophenotype/uberon/actions/runs/28838614182
|
Done. Summary of changes on 1. Synchronized with
2. Removed empty template
3. Updated
4. Added the two NTR terms to
The edit file was reserialised via 🤖 Generated by @dragon-ai-agent
|
|
Claude finished @dragon-ai-agent's task in 3m 11s —— View job PR Review — Add HRA Kidney NTR Template (2 New Terms)Checklist:
Summary of latest update (commit
|
|
Note: this run was launched in parallel with run 28838614182, which finished first and pushed the changes to 🤖 Generated by @dragon-ai-agent
|
There was a problem hiding this comment.
Checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate (one gap remains)
- Obsolete or replacement handling is safe (N/A — no obsoletions)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Latest update (commit 0c5ad43) resolves the empty-file removal, synonym addition, and adds both terms directly to src/ontology/uberon-edit.obo with correct parents (UBERON:0001473, UBERON:0002113, UBERON:0000483, UBERON:0009095 all verified) and metadata.
The earlier CRITICAL about registering the templates in uberon-odk.yaml is now superseded rather than fixed as literally suggested: since the terms are asserted directly in uberon-edit.obo, wiring hra-kidney.template.tsv into uberon-odk.yaml now would duplicate UBERON:8930105/UBERON:8930106 across two merged sources. Leaving it unregistered is correct.
Remaining 🟡 IMPORTANT: UBERON:8930106 (epithelium of tip of renal papilla) still cites only an ASCTB-TEMP placeholder IRI as its def_xref, with no real PMID/DOI. This was flagged in the original review and acknowledged as a known gap in the PR description. Recommend adding a real citation before merge.
Everything else looks ready to merge once that reference is added.
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
|
Claude finished @dosumis's task in 3m 25s —— View job PR Review — Add HRA Kidney NTR Template (2 New Terms)Checklist:
Todo List:
Summary of latest push (
|
|
Reports relocated. Route: manual hand-edit (2 terms, <20). TODO before converting into
Automated update (@cellsemantic / dragon-ai-agent, for @dosumis). Reports were relocated out of |
| [Term] | ||
| id: UBERON:8930106 | ||
| name: epithelium of tip of renal papilla | ||
| def: "An epithelium that lines the tip of the renal papilla where it projects into the minor calyx. This epithelial layer consists of transitional epithelium (urothelium) that marks the transition from the simple epithelium of the collecting ducts to the urothelium that lines the urinary collecting system, including the calyces, renal pelvis, and ureters." [https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium] |
There was a problem hiding this comment.
🟡 IMPORTANT: def_xref for UBERON:8930106 (epithelium of tip of renal papilla) is still only the ASCTB-TEMP placeholder IRI (https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium) — no real PMID/DOI/ISBN. This has been flagged in both prior review rounds and is acknowledged as a known gap in the PR description. Per the NTR workflow QC checklist, every term needs a real citable reference. Please add a PMID/DOI here and in the matching row of src/templates/hra-kidney.template.tsv before merge (or as an immediate fast-follow).
There was a problem hiding this comment.
PR Review — Add HRA Kidney NTR Template (2 New Terms)
Checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate (one gap remains)
- Obsolete or replacement handling is safe (N/A — no obsoletions)
- OBO and ODK conventions appear preserved
- No obvious CI, auth, or workflow regression
Re-reviewed after commit b2ad312 (moved workflow report artifacts from src/templates/ to bulk_ntr_workflow/outputs/hra-kidney-reports/ — no ontology content changed).
Verified: UBERON:8930105 and UBERON:8930106 each appear once in uberon-edit.obo, both IDs fall within idrange:42 (allocated to Jie Zheng), and all four parent terms (UBERON:0001473, UBERON:0002113, UBERON:0000483, UBERON:0009095) exist and are logically appropriate.
🟡 IMPORTANT (unresolved, carried over from earlier rounds): UBERON:8930106 ("epithelium of tip of renal papilla") still cites only the ASCTB-TEMP placeholder IRI as its def_xref, in both uberon-edit.obo and hra-kidney.template.tsv. No real PMID/DOI/ISBN has been added, and the PR description still acknowledges this gap. Left an inline comment on the specific line. Recommend adding a real reference before merge.
Everything else looks ready to merge once that reference is added.
| name: kidney lymphatic vessel | ||
| def: "A lymphatic vessel that is part of a kidney." [https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel, PMID:24065628] | ||
| subset: added_by_HRA | ||
| is_a: UBERON:0001473 ! lymphatic vessel |
There was a problem hiding this comment.
@zhengj2007 this is a grouping term so should have necessary and sufficient (intersection_of / EquivalentClass) definition.
PMID:24065628 does not look like a relevant ref
If we include https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel - should be plain xref only (perhaps as curie?) - it's not a definition reference.
| @@ -0,0 +1,4 @@ | |||
| ID LABEL Definition def_xref synonym is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref | |||
There was a problem hiding this comment.
Presumably this file is no longer needed and can be deleted?
|
Claude finished @dosumis's task in 4m 59s —— View job PR Review — Add HRA Kidney NTR Template (2 New Terms)Checklist:
Todo List:
SummaryRe-reviewing after @dosumis's latest inline feedback on commit 🔴 CRITICAL1. Both new terms lack a necessary-and-sufficient ( (the asserted 2. 🟡 IMPORTANT3. ASCTB-TEMP placeholder IRIs are inside the 4. 🔵 SUGGESTION5. What looks good
RecommendationTwo 🔴 CRITICAL and two 🟡 IMPORTANT issues remain open (logical definitions, a misattributed PMID, and the missing real reference for |
| [Term] | ||
| id: UBERON:8930105 | ||
| name: kidney lymphatic vessel | ||
| def: "A lymphatic vessel that is part of a kidney." [https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel, PMID:24065628] |
There was a problem hiding this comment.
🔴 CRITICAL: PMID:24065628 does not appear to be a relevant reference for "kidney lymphatic vessel". I checked every other place this PMID is cited in uberon-edit.obo — it supports UBERON:8480016 (perirenal space), UBERON:8480017 (anterior pararenal space), UBERON:8480018 (posterior pararenal space), UBERON:8480020 (perivesical space), and UBERON:8480021 (prevesical space). All of these are about retroperitoneal/pararenal fascial compartments, not lymphatics. This strongly suggests the PMID was copied from an adjacent ASCT+B row rather than sourced for this term, and should be replaced with a real reference specifically supporting renal lymphatic vessel anatomy (or dropped if none can be found, leaving only a provenance xref — see next comment).
Separately (per @dosumis): the https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel IRI is a provenance/mapping identifier, not a definition source, and shouldn't be inside the def_xref brackets. Move it to a plain xref: line instead, e.g.:
def: "A lymphatic vessel that is part of a kidney." [PMID:<real-ref>]
...
xref: https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel
| name: kidney lymphatic vessel | ||
| def: "A lymphatic vessel that is part of a kidney." [https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel, PMID:24065628] | ||
| subset: added_by_HRA | ||
| is_a: UBERON:0001473 ! lymphatic vessel |
There was a problem hiding this comment.
🔴 CRITICAL (per @dosumis): this is a compositional "X of organ" grouping term and should have a necessary-and-sufficient (genus-differentia) definition via intersection_of, not an asserted is_a + relationship: part_of. This is the established convention elsewhere in Uberon for the same shape of term — e.g. UBERON:0001902 (epithelium of small intestine) uses:
intersection_of: UBERON:0000483 ! epithelium
intersection_of: part_of UBERON:0002108 ! small intestine
and most other <organ> lymphatic vessel terms use intersection_of: UBERON:0001473 ! lymphatic vessel rather than asserted is_a.
Recommend replacing:
is_a: UBERON:0001473 ! lymphatic vessel
...
relationship: part_of UBERON:0002113 ! kidney
with:
intersection_of: UBERON:0001473 ! lymphatic vessel
intersection_of: part_of UBERON:0002113 ! kidney
(per CLAUDE.md, the reasoner infers the most specific is_a, so it's fine to omit the asserted is_a line once intersection_of is added). The same fix applies to UBERON:8930106 below, which has the identical is_a/relationship structure.
| [Term] | ||
| id: UBERON:8930106 | ||
| name: epithelium of tip of renal papilla | ||
| def: "An epithelium that lines the tip of the renal papilla where it projects into the minor calyx. This epithelial layer consists of transitional epithelium (urothelium) that marks the transition from the simple epithelium of the collecting ducts to the urothelium that lines the urinary collecting system, including the calyces, renal pelvis, and ureters." [https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium] |
There was a problem hiding this comment.
🟡 IMPORTANT (carried over from prior review rounds, still unresolved): def_xref for UBERON:8930106 is still only the ASCTB-TEMP placeholder IRI — no real PMID/DOI/ISBN. Per @dosumis's latest comment, the ASCTB-TEMP IRI shouldn't be in the def_xref bracket at all (it's provenance, not a definition source) — so once it's moved to a plain xref: line (consistent with the fix suggested for UBERON:8930105 above), this term would have zero def_xref entries. A real citable reference for the urothelium/collecting-duct transition at the renal papilla tip is needed before merge.
| subset: added_by_HRA | ||
| synonym: "papillary tip epithelium" RELATED [] | ||
| xref: Wikipedia:Renal_papilla | ||
| is_a: UBERON:0000483 ! epithelium |
There was a problem hiding this comment.
🔴 CRITICAL: same issue as UBERON:8930105 above — this grouping term should use intersection_of for a necessary-and-sufficient definition rather than asserted is_a + relationship: part_of:
intersection_of: UBERON:0000483 ! epithelium
intersection_of: part_of UBERON:0009095 ! tip of renal papilla
| @@ -0,0 +1,4 @@ | |||
| ID LABEL Definition def_xref synonym is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref | |||
There was a problem hiding this comment.
🔵 SUGGESTION (per @dosumis): since both terms were hand-added directly to src/ontology/uberon-edit.obo (per the batch-size policy noted upthread: <20 new terms → hand-edit rather than ODK-register), this ROBOT template is no longer wired into the build (confirmed: not registered in uberon-odk.yaml) and now only duplicates information already in the edit file. Recommend deleting it, similar to how the hra-kidney-groups.template.tsv and report artifacts were already cleaned up earlier in this PR.
There was a problem hiding this comment.
PR Review — Add HRA Kidney NTR Template (2 New Terms)
Checklist:
- Hierarchy and parents are consistent
- Definitions and supporting references look adequate — two blockers found
- Obsolete or replacement handling is safe (N/A — no obsoletions)
- OBO and ODK conventions appear preserved — logical definition issue found
- No obvious CI, auth, or workflow regression
Re-reviewed after @dosumis's latest inline feedback (commit a8bf41a). See inline comments for details.
🔴 CRITICAL
- UBERON:8930105 and UBERON:8930106 lack a necessary-and-sufficient (intersection_of) logical definition — both use asserted is_a + relationship: part_of instead of the standard genus-differentia intersection_of pattern used elsewhere in Uberon for this term shape (e.g. UBERON:0001902 epithelium of small intestine).
- PMID:24065628 is not a relevant reference for "kidney lymphatic vessel" — verified independently that every other citation of this PMID in uberon-edit.obo (UBERON:8480016/17/18/20/21) supports retroperitoneal/pararenal fascial-space terms, not lymphatics. Looks misattributed.
🟡 IMPORTANT
3. ASCTB-TEMP placeholder IRIs are inside the def_xref brackets for both terms — should be plain xref lines, not definition sources.
4. UBERON:8930106 still has no real citable PMID/DOI (only the ASCTB-TEMP IRI) — flagged in every prior review round; becomes a total gap once point 3 is fixed.
🔵 SUGGESTION
5. src/templates/hra-kidney.template.tsv looks orphaned now that both terms are hand-added directly to uberon-edit.obo (not registered in uberon-odk.yaml) — consider deleting it.
Everything else (ID range, parents, contributor/date/taxon metadata, synonym capture, report-artifact relocation) looks correct.
4 participants
Generated via bulk_ntr_workflow from source_data/kidney.csv:
'epithelium of tip of renal papilla'
Note: kidney lymphatic vessel includes PMID:24065628; papillary tip epithelium still needs curator-supplied PMID/DOI beyond ASCTB/Wikipedia references.