From 0849fb48ae33b0dd7f5fb1b1367ac1f553fdaa89 Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Tue, 26 May 2026 09:29:44 -0400 Subject: [PATCH 1/3] Add HRA kidney NTR template (2 new terms) 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 --- bulk_ntr_workflow/source_data/kidney.csv | 3 +++ src/templates/hra-kidney-groups.template.tsv | 2 ++ src/templates/hra-kidney-reports/candidates.tsv | 1 + src/templates/hra-kidney-reports/errors.tsv | 1 + src/templates/hra-kidney-reports/input.tsv | 3 +++ src/templates/hra-kidney-reports/name_corrections.tsv | 2 ++ src/templates/hra-kidney.template.tsv | 4 ++++ 7 files changed, 16 insertions(+) create mode 100644 bulk_ntr_workflow/source_data/kidney.csv create mode 100644 src/templates/hra-kidney-groups.template.tsv create mode 100644 src/templates/hra-kidney-reports/candidates.tsv create mode 100644 src/templates/hra-kidney-reports/errors.tsv create mode 100644 src/templates/hra-kidney-reports/input.tsv create mode 100644 src/templates/hra-kidney-reports/name_corrections.tsv create mode 100644 src/templates/hra-kidney.template.tsv diff --git a/bulk_ntr_workflow/source_data/kidney.csv b/bulk_ntr_workflow/source_data/kidney.csv new file mode 100644 index 000000000..b54697f99 --- /dev/null +++ b/bulk_ntr_workflow/source_data/kidney.csv @@ -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, \ No newline at end of file diff --git a/src/templates/hra-kidney-groups.template.tsv b/src/templates/hra-kidney-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-kidney-groups.template.tsv @@ -0,0 +1,2 @@ +ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| diff --git a/src/templates/hra-kidney-reports/candidates.tsv b/src/templates/hra-kidney-reports/candidates.tsv new file mode 100644 index 000000000..6db5d8134 --- /dev/null +++ b/src/templates/hra-kidney-reports/candidates.tsv @@ -0,0 +1 @@ +label as_iri uberon_id note diff --git a/src/templates/hra-kidney-reports/errors.tsv b/src/templates/hra-kidney-reports/errors.tsv new file mode 100644 index 000000000..7f20612cf --- /dev/null +++ b/src/templates/hra-kidney-reports/errors.tsv @@ -0,0 +1 @@ +label as_iri issue_type parent_id parent_label detail diff --git a/src/templates/hra-kidney-reports/input.tsv b/src/templates/hra-kidney-reports/input.tsv new file mode 100644 index 000000000..cfe406e87 --- /dev/null +++ b/src/templates/hra-kidney-reports/input.tsv @@ -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 diff --git a/src/templates/hra-kidney-reports/name_corrections.tsv b/src/templates/hra-kidney-reports/name_corrections.tsv new file mode 100644 index 000000000..3897a673b --- /dev/null +++ b/src/templates/hra-kidney-reports/name_corrections.tsv @@ -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. diff --git a/src/templates/hra-kidney.template.tsv b/src/templates/hra-kidney.template.tsv new file mode 100644 index 000000000..b8ae63efc --- /dev/null +++ b/src/templates/hra-kidney.template.tsv @@ -0,0 +1,4 @@ +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_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 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 From 0c5ad434baf6e39c50f0b8024b8b6b43744161d5 Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Tue, 7 Jul 2026 03:21:39 +0000 Subject: [PATCH 2/3] Sync branch with master, tidy templates, and add NTR terms to uberon-edit.obo MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - 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 --- src/ontology/uberon-edit.obo | 26 ++++++++++++++++++++ src/templates/hra-kidney-groups.template.tsv | 2 -- src/templates/hra-kidney.template.tsv | 8 +++--- 3 files changed, 30 insertions(+), 6 deletions(-) delete mode 100644 src/templates/hra-kidney-groups.template.tsv diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 240b86a5b..08f965bed 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225242,6 +225242,32 @@ 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] +subset: added_by_HRA +is_a: UBERON:0001473 ! lymphatic vessel +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 +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] +subset: added_by_HRA +synonym: "papillary tip epithelium" RELATED [] +xref: Wikipedia:Renal_papilla +is_a: UBERON:0000483 ! epithelium +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 diff --git a/src/templates/hra-kidney-groups.template.tsv b/src/templates/hra-kidney-groups.template.tsv deleted file mode 100644 index dff359c07..000000000 --- a/src/templates/hra-kidney-groups.template.tsv +++ /dev/null @@ -1,2 +0,0 @@ -ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref -ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| diff --git a/src/templates/hra-kidney.template.tsv b/src/templates/hra-kidney.template.tsv index b8ae63efc..15beb680d 100644 --- a/src/templates/hra-kidney.template.tsv +++ b/src/templates/hra-kidney.template.tsv @@ -1,4 +1,4 @@ -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_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 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 +ID LABEL Definition def_xref synonym 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=| 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 From b2ad3122588db1f7489baf8af53fca89429c2345 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 6 Jul 2026 16:04:43 +0100 Subject: [PATCH 3/3] Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/ 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 --- .../outputs}/hra-kidney-reports/candidates.tsv | 0 .../outputs}/hra-kidney-reports/errors.tsv | 0 .../outputs}/hra-kidney-reports/input.tsv | 0 .../outputs}/hra-kidney-reports/name_corrections.tsv | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename {src/templates => bulk_ntr_workflow/outputs}/hra-kidney-reports/candidates.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-kidney-reports/errors.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-kidney-reports/input.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-kidney-reports/name_corrections.tsv (100%) diff --git a/src/templates/hra-kidney-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-kidney-reports/candidates.tsv similarity index 100% rename from src/templates/hra-kidney-reports/candidates.tsv rename to bulk_ntr_workflow/outputs/hra-kidney-reports/candidates.tsv diff --git a/src/templates/hra-kidney-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-kidney-reports/errors.tsv similarity index 100% rename from src/templates/hra-kidney-reports/errors.tsv rename to bulk_ntr_workflow/outputs/hra-kidney-reports/errors.tsv diff --git a/src/templates/hra-kidney-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-kidney-reports/input.tsv similarity index 100% rename from src/templates/hra-kidney-reports/input.tsv rename to bulk_ntr_workflow/outputs/hra-kidney-reports/input.tsv diff --git a/src/templates/hra-kidney-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/hra-kidney-reports/name_corrections.tsv similarity index 100% rename from src/templates/hra-kidney-reports/name_corrections.tsv rename to bulk_ntr_workflow/outputs/hra-kidney-reports/name_corrections.tsv