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Add HRA intestine/liver/skin NTR template (4 new terms) #3716

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Add HRA intestine/liver/skin NTR template (4 new terms) #3716

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6 changes: 6 additions & 0 deletions bulk_ntr_workflow/source_data/intestine-liver-skin.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
large-intestine,https://purl.org/ccf/ASCTB-TEMP_free-coli,free coli,,,UBERON:0012419,taenia coli,"ISBN:978-1496398949, isBN:978-1496398949"
large-intestine,https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli,mesocolic coli,,,UBERON:0012419,taenia coli,"ISBN:978-1496398949, isBN:978-1496398949"
large-intestine,https://purl.org/ccf/ASCTB-TEMP_omental-coli,omental coli,,,UBERON:0012419,taenia coli,"ISBN:978-1496398949, isBN:978-1496398949"
liver,https://purl.org/ccf/ASCTB-TEMP_liver-immune-resident-component,Liver immune resident component,,,UBERON:0004647,liver lobule,"https://doi.org/10.1111/imm.12888, https://doi.org/10.1172/jci.insight.90063, https://doi.org/10.3389/fimmu.2019.01502"
skin,https://purl.org/ccf/ASCTB-TEMP_connective-tissue-sheath,connective tissue sheath,,,UBERON:0002073,hair follicle,
2 changes: 2 additions & 0 deletions src/templates/hra-intestine-liver-skin-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=|
1 change: 1 addition & 0 deletions src/templates/hra-intestine-liver-skin-reports/candidates.tsv
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label as_iri uberon_id note
1 change: 1 addition & 0 deletions src/templates/hra-intestine-liver-skin-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
6 changes: 6 additions & 0 deletions src/templates/hra-intestine-liver-skin-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
large-intestine https://purl.org/ccf/ASCTB-TEMP_free-coli free coli UBERON:0012419 taenia coli ISBN:978-1496398949, isBN:978-1496398949 leaf
large-intestine https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli mesocolic coli UBERON:0012419 taenia coli ISBN:978-1496398949, isBN:978-1496398949 leaf
large-intestine https://purl.org/ccf/ASCTB-TEMP_omental-coli omental coli UBERON:0012419 taenia coli ISBN:978-1496398949, isBN:978-1496398949 leaf
liver https://purl.org/ccf/ASCTB-TEMP_liver-immune-resident-component Liver immune resident component UBERON:0004647 liver lobule https://doi.org/10.1111/imm.12888, https://doi.org/10.1172/jci.insight.90063, https://doi.org/10.3389/fimmu.2019.01502 leaf
skin https://purl.org/ccf/ASCTB-TEMP_connective-tissue-sheath connective tissue sheath UBERON:0002073 hair follicle leaf
4 changes: 4 additions & 0 deletions src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv
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source_label corrected_label reason
free coli free taenia coli Standard anatomical nomenclature uses 'taenia coli' for the longitudinal muscle bands of the colon. The term 'coli' alone is incomplete. Wikipedia and anatomical literature refer to this as 'free taenia coli' or 'taenia libera'. The source term 'free coli' should be added as a synonym.
mesocolic coli mesocolic taenia coli Standard anatomical nomenclature uses 'taenia coli' for the longitudinal muscle bands of the colon. The term 'coli' alone is incomplete. Wikipedia and anatomical literature refer to this as 'mesocolic taenia coli' or 'taenia mesocolica'. The source term 'mesocolic coli' should be added as a synonym.
omental coli omental taenia coli Standard anatomical nomenclature uses 'taenia coli' for the longitudinal muscle bands of the colon. The term 'coli' alone is incomplete. Wikipedia and anatomical literature refer to this as 'omental taenia coli' or 'taenia omentalis'. The source term 'omental coli' should be added as a synonym.
2 changes: 2 additions & 0 deletions src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv
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label reason suggestion
Liver immune resident component This term describes a functional population of immune cells residing in the liver, not an anatomical structure or structural subdivision. UBERON covers anatomical structures, while cellular populations and immune cell types belong in the Cell Ontology (CL) or specialized immunology ontologies. While liver lobule (UBERON:0004647) is a valid anatomical structure, 'immune resident component' refers to the collection of immune cells (Kupffer cells, NK cells, NKT cells, dendritic cells) that inhabit liver tissue - this is a cellular/immunological classification rather than a structural subdivision. This term should be represented in the Cell Ontology (CL) or as a defined class using CL terms with 'part_of some liver' or 'part_of some liver lobule' relationships. The three DOI references (10.1111/imm.12888, 10.1172/jci.insight.90063, 10.3389/fimmu.2019.01502) are immunology papers that would be appropriate for CL term definitions describing liver-resident immune cell populations. If an anatomical term is needed, consider whether the source data refers to a distinct anatomical compartment (like 'portal tract' UBERON:0001282) rather than a cell population.
6 changes: 6 additions & 0 deletions src/templates/hra-intestine-liver-skin.template.tsv
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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_8930100 free taenia coli An organ component layer composed primarily of smooth muscle that forms one of the three longitudinal ribbons (taeniae) of the colon musculature, positioned anteriorly in the cecum, ascending colon, descending colon, and sigmoid colon, and inferiorly in the transverse colon. ISBN:978-1496398949|isBN:978-1496398949|https://purl.org/ccf/ASCTB-TEMP_free-coli|PMID:29218384|PMID:30324463 UBERON:0004923 UBERON:0012419 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Taenia_coli
http://purl.obolibrary.org/obo/UBERON_8930101 mesocolic taenia coli An organ component layer composed primarily of smooth muscle that forms one of the three longitudinal ribbons (taeniae) of the colon musculature, present on the posteromedial surface of the cecum, ascending colon, descending colon, and sigmoid colon, and positioned posteriorly on the transverse colon at the site of attachment of the transverse mesocolon. ISBN:978-1496398949|isBN:978-1496398949|https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli|PMID:29218384|PMID:30324463 UBERON:0004923 UBERON:0012419 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Taenia_coli
http://purl.obolibrary.org/obo/UBERON_8930102 omental taenia coli An organ component layer composed primarily of smooth muscle that forms one of the three longitudinal ribbons (taeniae) of the colon musculature, situated posterolaterally in the cecum, ascending colon, descending colon, and sigmoid colon, and on the anterosuperior surface of the transverse colon where layers three and four of the greater omentum meet the transverse colon. ISBN:978-1496398949|isBN:978-1496398949|https://purl.org/ccf/ASCTB-TEMP_omental-coli|PMID:29218384|PMID:30324463 UBERON:0004923 UBERON:0012419 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Taenia_coli
http://purl.obolibrary.org/obo/UBERON_8930104 connective tissue sheath A layer of connective tissue that surrounds the epithelial components of the hair follicle, providing structural support and containing fibroblasts and extracellular matrix proteins including type I collagen. https://purl.org/ccf/ASCTB-TEMP_connective-tissue-sheath|PMID:23036740|PMID:2078047 UBERON:0002384 UBERON:0002073 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Hair_follicle
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