Skip to content

Add HRA kidney NTR template (2 new terms) #3717

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
zhengj2007 wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Add HRA kidney NTR template (2 new terms) #3717

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
0849fb4
Add HRA kidney NTR template (2 new terms)
zhengj2007 May 26, 2026
812b6b5
Merge remote-tracking branch 'origin/master' into add-hra-kidney-ntr
dragon-ai-agent Jul 7, 2026
0c5ad43
Sync branch with master, tidy templates, and add NTR terms to uberon-…
dragon-ai-agent Jul 7, 2026
b2ad312
Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/
dosumis Jul 6, 2026
b76e7fb
Merge branch 'master' into add-hra-kidney-ntr
dosumis Jul 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions bulk_ntr_workflow/outputs/hra-kidney-reports/candidates.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
label as_iri uberon_id note
1 change: 1 addition & 0 deletions bulk_ntr_workflow/outputs/hra-kidney-reports/errors.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
label as_iri issue_type parent_id parent_label detail
3 changes: 3 additions & 0 deletions bulk_ntr_workflow/outputs/hra-kidney-reports/input.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
table as_iri label uberon_id parent_id parent_label references term_type
https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel kidney lymphatic vessel UBERON:0006544 kidney vasculature leaf
https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium Papillary Tip Epithelium UBERON:0009095 tip of renal papilla leaf
2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/hra-kidney-reports/name_corrections.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
source_label corrected_label reason
Papillary Tip Epithelium epithelium of tip of renal papilla UBERON convention uses 'epithelium of X' pattern rather than 'X Epithelium'. The corrected name follows the standard anatomical naming pattern seen in similar UBERON terms like 'epithelium of lung', 'epithelium of colon'. Keep source name as synonym.
3 changes: 3 additions & 0 deletions bulk_ntr_workflow/source_data/kidney.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
kidney,https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel,kidney lymphatic vessel,,,UBERON:0006544,kidney vasculature,
kidney,https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium,Papillary Tip Epithelium,,,UBERON:0009095,tip of renal papilla,
26 changes: 26 additions & 0 deletions src/ontology/uberon-edit.obo
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -225244,6 +225244,32 @@ is_a: UBERON:0006914 ! squamous epithelium
relationship: has_part CL:4030023 ! respiratory tract hillock cell
relationship: part_of UBERON:0007196 ! tracheobronchial tree

[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]

@dosumis dosumis Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@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.

@ai4c-agent ai4c-agent Bot Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🔴 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

subset: added_by_HRA
is_a: UBERON:0001473 ! lymphatic vessel

@ai4c-agent ai4c-agent Bot Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🔴 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.

relationship: dc-contributor https://orcid.org/0000-0002-2999-0103
relationship: in_taxon NCBITaxon:9606 ! Homo sapiens
relationship: part_of UBERON:0002113 ! kidney
property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime
property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3717" xsd:anyURI

[Term]
id: UBERON:8930106

@ai4c-agent ai4c-agent Bot Jul 9, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🟡 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).

Fix this →

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]

@ai4c-agent ai4c-agent Bot Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🟡 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

@ai4c-agent ai4c-agent Bot Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🔴 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

relationship: dc-contributor https://orcid.org/0000-0002-2999-0103
relationship: in_taxon NCBITaxon:9606 ! Homo sapiens
relationship: part_of UBERON:0009095 ! tip of renal papilla
property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime
property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3717" xsd:anyURI

[Typedef]
id: aboral_to
name: aboral to
Expand Down
4 changes: 4 additions & 0 deletions src/templates/hra-kidney.template.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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

@dosumis dosumis Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Presumably this file is no longer needed and can be deleted?

@ai4c-agent ai4c-agent Bot Jul 27, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🔵 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.

ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| A oboInOwl:hasRelatedSynonym 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_8930105 kidney lymphatic vessel A lymphatic vessel that is part of a kidney. https://purl.org/ccf/ASCTB-TEMP_kidney-lymphatic-vessel|PMID:24065628 UBERON:0001473 UBERON:0002113 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
http://purl.obolibrary.org/obo/UBERON_8930106 epithelium of tip of renal papilla 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 papillary tip epithelium UBERON:0000483 UBERON:0009095 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:Renal_papilla
Loading