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Add HRA uterus NTR batch outputs and review reports #3723

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d4de247
Add HRA uterus NTR batch outputs and review reports
zhengj2007 May 26, 2026
f82ed04
Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/
dosumis Jul 6, 2026
30d1ad3
Register hra_uterus as ODK component (27 leaf terms)
dosumis Jul 9, 2026
48dee58
Regenerate ODK Makefile to wire hra_uterus component (make update_repo)
dosumis Jul 9, 2026
9e7e1b3
Merge branch 'master' into add-hra-uterus-ntr
zhengj2007 Jul 19, 2026
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7 changes: 7 additions & 0 deletions bulk_ntr_workflow/outputs/hra-uterus-reports/candidates.tsv
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label as_iri uberon_id note
cervical mucosa UBERON:0012248 confirmed_match (confidence: high)
cervical os UBERON:0013758 confirmed_match (confidence: high)
cervical squamo-columnar junction UBERON:0012253 confirmed_match (confidence: high)
internal cervical os UBERON:0013759 confirmed_match (confidence: high)
ectocervical epithelium UBERON:0012251 confirmed_match (confidence: high)
external cervical os UBERON:0013760 confirmed_match (confidence: high)
13 changes: 13 additions & 0 deletions bulk_ntr_workflow/outputs/hra-uterus-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
central anterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_central-anterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
central anterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_central-anterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
central posterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_central-posterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
central posterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_central-posterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
left anterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_left-anterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
left anterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_left-anterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
left posterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_left-posterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
left posterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_left-posterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
right anterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_right-anterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
right anterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_right-anterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
right posterior fundus of uterus https://purl.org/ccf/ASCTB-TEMP_right-posterior-fundus-of-uterus unknown_parent FMA:17561 Fundus of uterus Unrecognised parent ID format
right posterior lower uterine segment https://purl.org/ccf/ASCTB-TEMP_right-posterior-lower-uterine-segment unknown_parent lower uterine segment Unrecognised parent ID format
35 changes: 35 additions & 0 deletions bulk_ntr_workflow/outputs/hra-uterus-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
uterus https://purl.org/ccf/ASCTB-TEMP_central-anterior-body-of-uterus central anterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_central-anterior-fundus-of-uterus central anterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_central-anterior-lower-uterine-segment central anterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_central-posterior-body-of-uterus central posterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_central-posterior-fundus-of-uterus central posterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_central-posterior-lower-uterine-segment central posterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_cervical-mucosa cervical mucosa UBERON:0000002 uterine cervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_cervical-os cervical os UBERON:0000002 uterine cervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_cervical-squamo-columnar-junction cervical squamo-columnar junction UBERON:0000002 uterine cervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_columnar-cell-of-endocervix columnar cell of endocervix UBERON:0000458 endocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_connective-tissue-of-the-uterine-serosa connective tissue of the uterine serosa UBERON:0001297 serosa of the uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_ectocervical-epithelium ectocervical epithelium UBERON:0012249 ectocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_ectocervical-stroma ectocervical stroma UBERON:0012249 ectocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_endocervical-stroma endocervical stroma UBERON:0000458 endocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_external-cervical-os external cervical os UBERON:0012249 ectocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_inferior-uterine-vein inferior uterine vein UBERON:0000995 uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_inner-uterine-myometrium inner uterine myometrium UBERON:0001296 uterine myometrium https://doi.org/10.1093/molehr/gat083, https://doi.org/10.1186/1471-2393-13-S1-S7 leaf
uterus https://purl.org/ccf/ASCTB-TEMP_internal-cervical-os internal cervical os UBERON:0000458 endocervix leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-anterior-body-of-uterus left anterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-anterior-fundus-of-uterus left anterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-anterior-lower-uterine-segment left anterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-posterior-body-of-uterus left posterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-posterior-fundus-of-uterus left posterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_left-posterior-lower-uterine-segment left posterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_lower-uterine-segment lower uterine segment UBERON:0000995 uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_mesothelium-of-the-uterine-serosa mesothelium of the uterine serosa UBERON:0001297 serosa of the uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_outer-uterine-myometrium outer uterine myometrium UBERON:0001296 uterine myometrium https://doi.org/10.1101/2021.01.02.425073 leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-anterior-body-of-uterus right anterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-anterior-fundus-of-uterus right anterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-anterior-lower-uterine-segment right anterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-posterior-body-of-uterus right posterior body of uterus UBERON:0009853 body of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-posterior-fundus-of-uterus right posterior fundus of uterus FMA:17561 Fundus of uterus leaf
uterus https://purl.org/ccf/ASCTB-TEMP_right-posterior-lower-uterine-segment right posterior lower uterine segment lower uterine segment leaf
uterus https://purl.org/ccf/ASCTB-TEMP_superior-uterine-vein superior uterine vein UBERON:0000995 uterus leaf
2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/hra-uterus-reports/manual_curation.tsv
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label definition reason similar_terms suggestion
columnar cell of endocervix A columnar epithelial cell that is part of the endocervical mucosa, forming a single layer of mucinous columnar epithelium lining the cervical canal. Cell types typically belong in the Cell Ontology (CL), not UBERON. UBERON references cell types from CL (e.g., CL:0000075 'columnar/cuboidal epithelial cell') but generally does not define individual cell types directly. The term has been assigned a UBERON ID (UBERON_8930209), suggesting it should be added to UBERON, but this conflicts with standard ontology design patterns. CL:0000075=columnar/cuboidal epithelial cell; UBERON:0012252=endocervical epithelium; UBERON:0000485=simple columnar epithelium Options: (1) Route to Cell Ontology as 'endocervical columnar cell' with is_a: CL:0000075 and part_of: UBERON:0012252 (endocervical epithelium); (2) If keeping in UBERON, create import from CL:0000075 as genus and add intersection_of: CL:0000075, intersection_of: part_of UBERON:0012252; (3) Mark as a tissue-level term rather than cell-level by treating it as a subtype of endocervical epithelium. Recommend curator review for appropriate ontology placement.
36 changes: 36 additions & 0 deletions bulk_ntr_workflow/source_data/uterus.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
ureter,https://purl.org/ccf/ASCTB-TEMP_ureter-vasculature,ureter vasculature,,,UBERON:0036376,wall of left ureter,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-body-of-uterus,central anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-fundus-of-uterus,central anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-lower-uterine-segment,central anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-body-of-uterus,central posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-fundus-of-uterus,central posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-lower-uterine-segment,central posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-mucosa,cervical mucosa,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-os,cervical os,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-squamo-columnar-junction,cervical squamo-columnar junction,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_columnar-cell-of-endocervix,columnar cell of endocervix,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_connective-tissue-of-the-uterine-serosa,connective tissue of the uterine serosa,,,UBERON:0001297,serosa of the uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_ectocervical-epithelium,ectocervical epithelium,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_ectocervical-stroma,ectocervical stroma,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_endocervical-stroma,endocervical stroma,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_external-cervical-os,external cervical os,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_inferior-uterine-vein,inferior uterine vein,,,UBERON:0000995,uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_inner-uterine-myometrium,inner uterine myometrium,,,UBERON:0001296,uterine myometrium,"https://doi.org/10.1093/molehr/gat083, https://doi.org/10.1186/1471-2393-13-S1-S7"
uterus,https://purl.org/ccf/ASCTB-TEMP_internal-cervical-os,internal cervical os,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-body-of-uterus,left anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-fundus-of-uterus,left anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-lower-uterine-segment,left anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-body-of-uterus,left posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-fundus-of-uterus,left posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-lower-uterine-segment,left posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_lower-uterine-segment,lower uterine segment,,,UBERON:0000995,uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_mesothelium-of-the-uterine-serosa,mesothelium of the uterine serosa,,,UBERON:0001297,serosa of the uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_outer-uterine-myometrium,outer uterine myometrium,,,UBERON:0001296,uterine myometrium,https://doi.org/10.1101/2021.01.02.425073
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-body-of-uterus,right anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-fundus-of-uterus,right anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-lower-uterine-segment,right anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-body-of-uterus,right posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-fundus-of-uterus,right posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-lower-uterine-segment,right posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_superior-uterine-vein,superior uterine vein,,,UBERON:0000995,uterus,
35 changes: 35 additions & 0 deletions bulk_ntr_workflow/source_data/uterus_only.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-body-of-uterus,central anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-fundus-of-uterus,central anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-anterior-lower-uterine-segment,central anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-body-of-uterus,central posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-fundus-of-uterus,central posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_central-posterior-lower-uterine-segment,central posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-mucosa,cervical mucosa,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-os,cervical os,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_cervical-squamo-columnar-junction,cervical squamo-columnar junction,,,UBERON:0000002,uterine cervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_columnar-cell-of-endocervix,columnar cell of endocervix,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_connective-tissue-of-the-uterine-serosa,connective tissue of the uterine serosa,,,UBERON:0001297,serosa of the uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_ectocervical-epithelium,ectocervical epithelium,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_ectocervical-stroma,ectocervical stroma,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_endocervical-stroma,endocervical stroma,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_external-cervical-os,external cervical os,,,UBERON:0012249,ectocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_inferior-uterine-vein,inferior uterine vein,,,UBERON:0000995,uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_inner-uterine-myometrium,inner uterine myometrium,,,UBERON:0001296,uterine myometrium,"https://doi.org/10.1093/molehr/gat083, https://doi.org/10.1186/1471-2393-13-S1-S7"
uterus,https://purl.org/ccf/ASCTB-TEMP_internal-cervical-os,internal cervical os,,,UBERON:0000458,endocervix,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-body-of-uterus,left anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-fundus-of-uterus,left anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-anterior-lower-uterine-segment,left anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-body-of-uterus,left posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-fundus-of-uterus,left posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_left-posterior-lower-uterine-segment,left posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_lower-uterine-segment,lower uterine segment,,,UBERON:0000995,uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_mesothelium-of-the-uterine-serosa,mesothelium of the uterine serosa,,,UBERON:0001297,serosa of the uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_outer-uterine-myometrium,outer uterine myometrium,,,UBERON:0001296,uterine myometrium,https://doi.org/10.1101/2021.01.02.425073
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-body-of-uterus,right anterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-fundus-of-uterus,right anterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-anterior-lower-uterine-segment,right anterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-body-of-uterus,right posterior body of uterus,,,UBERON:0009853,body of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-fundus-of-uterus,right posterior fundus of uterus,,,FMA:17561,Fundus of uterus,
uterus,https://purl.org/ccf/ASCTB-TEMP_right-posterior-lower-uterine-segment,right posterior lower uterine segment,,,,lower uterine segment,
uterus,https://purl.org/ccf/ASCTB-TEMP_superior-uterine-vein,superior uterine vein,,,UBERON:0000995,uterus,
2 changes: 2 additions & 0 deletions src/templates/hra-uterus-groups.template.tsv
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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=|
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