From 306492f7946cecfa4df72c573e44b7f5acd849ab Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Mon, 25 May 2026 12:13:13 -0400 Subject: [PATCH 1/6] Add HRA intestine/liver/skin NTR template (4 new terms) Generated via bulk_ntr_workflow from source_data/intestine-liver-skin.csv (5 input rows from large-intestine, liver, and skin tables): - 4 new UBERON terms (UBERON:8930100-8930102, UBERON:8930104): - free taenia coli (UBERON:8930100) - mesocolic taenia coli (UBERON:8930101) - omental taenia coli (UBERON:8930102) - connective tissue sheath (UBERON:8930104) - of hair follicle - 1 row excluded as out-of-scope: 'Liver immune resident component' (functional immune-cell collective; belongs in CL, not UBERON) Name corrections applied: 'free coli' -> 'free taenia coli' etc. (source ASCTB labels were incomplete; full anatomical nomenclature used). Signed-off-by: dragon-ai-agent --- bulk_ntr_workflow/source_data/intestine-liver-skin.csv | 6 ++++++ src/templates/hra-intestine-liver-skin-groups.template.tsv | 2 ++ .../hra-intestine-liver-skin-reports/candidates.tsv | 1 + src/templates/hra-intestine-liver-skin-reports/errors.tsv | 1 + src/templates/hra-intestine-liver-skin-reports/input.tsv | 6 ++++++ .../hra-intestine-liver-skin-reports/name_corrections.tsv | 4 ++++ .../hra-intestine-liver-skin-reports/out_of_scope.tsv | 2 ++ src/templates/hra-intestine-liver-skin.template.tsv | 6 ++++++ 8 files changed, 28 insertions(+) create mode 100644 bulk_ntr_workflow/source_data/intestine-liver-skin.csv create mode 100644 src/templates/hra-intestine-liver-skin-groups.template.tsv create mode 100644 src/templates/hra-intestine-liver-skin-reports/candidates.tsv create mode 100644 src/templates/hra-intestine-liver-skin-reports/errors.tsv create mode 100644 src/templates/hra-intestine-liver-skin-reports/input.tsv create mode 100644 src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv create mode 100644 src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv create mode 100644 src/templates/hra-intestine-liver-skin.template.tsv diff --git a/bulk_ntr_workflow/source_data/intestine-liver-skin.csv b/bulk_ntr_workflow/source_data/intestine-liver-skin.csv new file mode 100644 index 000000000..0071b569a --- /dev/null +++ b/bulk_ntr_workflow/source_data/intestine-liver-skin.csv @@ -0,0 +1,6 @@ +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, \ No newline at end of file diff --git a/src/templates/hra-intestine-liver-skin-groups.template.tsv b/src/templates/hra-intestine-liver-skin-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-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-intestine-liver-skin-reports/candidates.tsv b/src/templates/hra-intestine-liver-skin-reports/candidates.tsv new file mode 100644 index 000000000..fe391472c --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-reports/candidates.tsv @@ -0,0 +1 @@ +label as_iri uberon_id note diff --git a/src/templates/hra-intestine-liver-skin-reports/errors.tsv b/src/templates/hra-intestine-liver-skin-reports/errors.tsv new file mode 100644 index 000000000..7f20612cf --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-reports/errors.tsv @@ -0,0 +1 @@ +label as_iri issue_type parent_id parent_label detail diff --git a/src/templates/hra-intestine-liver-skin-reports/input.tsv b/src/templates/hra-intestine-liver-skin-reports/input.tsv new file mode 100644 index 000000000..5165337af --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-reports/input.tsv @@ -0,0 +1,6 @@ +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 diff --git a/src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv b/src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv new file mode 100644 index 000000000..ec35c3afd --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv @@ -0,0 +1,4 @@ +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. diff --git a/src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv b/src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv new file mode 100644 index 000000000..6527ca410 --- /dev/null +++ b/src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv @@ -0,0 +1,2 @@ +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. diff --git a/src/templates/hra-intestine-liver-skin.template.tsv b/src/templates/hra-intestine-liver-skin.template.tsv new file mode 100644 index 000000000..793a71a1c --- /dev/null +++ b/src/templates/hra-intestine-liver-skin.template.tsv @@ -0,0 +1,6 @@ +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 From e4dc5928c5977efc3c006ef86f09fa4edb8d491f Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Mon, 6 Jul 2026 00:09:09 -0400 Subject: [PATCH 2/6] Normalize hra intestine/liver/skin template line endings @dragon-ai-agent --- src/templates/hra-intestine-liver-skin.template.tsv | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/templates/hra-intestine-liver-skin.template.tsv b/src/templates/hra-intestine-liver-skin.template.tsv index 793a71a1c..343048270 100644 --- a/src/templates/hra-intestine-liver-skin.template.tsv +++ b/src/templates/hra-intestine-liver-skin.template.tsv @@ -1,6 +1,6 @@ -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 +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|https://purl.org/ccf/ASCTB-TEMP_free-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_omental-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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 \ No newline at end of file From 9e0bb28a6aca5ffcd848df84f6bf9fdfbee50f74 Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Mon, 6 Jul 2026 00:18:28 -0400 Subject: [PATCH 3/6] Add HRA intestine/liver/skin OWL component Generate and serialize component in OWL Functional Syntax from template. @dragon-ai-agent --- src/templates/hra-intestine-liver-skin.owl | 83 +++++++++++++++++++ .../hra-intestine-liver-skin.template.tsv | 12 +-- 2 files changed, 89 insertions(+), 6 deletions(-) create mode 100644 src/templates/hra-intestine-liver-skin.owl diff --git a/src/templates/hra-intestine-liver-skin.owl b/src/templates/hra-intestine-liver-skin.owl new file mode 100644 index 000000000..c2754c43b --- /dev/null +++ b/src/templates/hra-intestine-liver-skin.owl @@ -0,0 +1,83 @@ +Prefix(obo:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) +Prefix(terms:=) +Prefix(oboInOwl:=) + + +Ontology( +Declaration(Class(obo:UBERON_0002384)) +Declaration(Class(obo:UBERON_0012419)) +Declaration(Class(obo:UBERON_8930100)) +Declaration(Class(obo:UBERON_8930101)) +Declaration(Class(obo:UBERON_8930102)) +Declaration(Class(obo:UBERON_8930104)) +Declaration(DataProperty(obo:BFO_0000050)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:RO_0002175)) +Declaration(AnnotationProperty(terms:contributor)) +Declaration(AnnotationProperty(terms:date)) +Declaration(AnnotationProperty(oboInOwl:hasDbXref)) +Declaration(AnnotationProperty(oboInOwl:inSubset)) +Declaration(Datatype(obo:UBERON_0002073)) +Declaration(Datatype(obo:UBERON_0011198)) + + + +############################ +# Classes +############################ + +# Class: obo:UBERON_8930100 (free taenia coli) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_free-coli") obo:IAO_0000115 obo:UBERON_8930100 "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.") +AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930100 obo:NCBITaxon_9606) +AnnotationAssertion(terms:contributor obo:UBERON_8930100 ) +AnnotationAssertion(terms:date obo:UBERON_8930100 "2026-05-25T00:00:00Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930100 "Wikipedia:Taenia_coli") +AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930100 ) +AnnotationAssertion(rdfs:label obo:UBERON_8930100 "free taenia coli") +SubClassOf(obo:UBERON_8930100 obo:UBERON_0012419) +SubClassOf(obo:UBERON_8930100 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) + +# Class: obo:UBERON_8930101 (mesocolic taenia coli) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli") obo:IAO_0000115 obo:UBERON_8930101 "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.") +AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930101 obo:NCBITaxon_9606) +AnnotationAssertion(terms:contributor obo:UBERON_8930101 ) +AnnotationAssertion(terms:date obo:UBERON_8930101 "2026-05-25T00:00:00Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930101 "Wikipedia:Taenia_coli") +AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930101 ) +AnnotationAssertion(rdfs:label obo:UBERON_8930101 "mesocolic taenia coli") +SubClassOf(obo:UBERON_8930101 obo:UBERON_0012419) +SubClassOf(obo:UBERON_8930101 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) + +# Class: obo:UBERON_8930102 (omental taenia coli) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_omental-coli") obo:IAO_0000115 obo:UBERON_8930102 "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.") +AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930102 obo:NCBITaxon_9606) +AnnotationAssertion(terms:contributor obo:UBERON_8930102 ) +AnnotationAssertion(terms:date obo:UBERON_8930102 "2026-05-25T00:00:00Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930102 "Wikipedia:Taenia_coli") +AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930102 ) +AnnotationAssertion(rdfs:label obo:UBERON_8930102 "omental taenia coli") +SubClassOf(obo:UBERON_8930102 obo:UBERON_0012419) +SubClassOf(obo:UBERON_8930102 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) + +# Class: obo:UBERON_8930104 (connective tissue sheath of hair follicle) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:2078047") Annotation(oboInOwl:hasDbXref "PMID:23036740") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_connective-tissue-sheath") obo:IAO_0000115 obo:UBERON_8930104 "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.") +AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930104 obo:NCBITaxon_9606) +AnnotationAssertion(terms:contributor obo:UBERON_8930104 ) +AnnotationAssertion(terms:date obo:UBERON_8930104 "2026-05-25T00:00:00Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930104 "Wikipedia:Hair_follicle") +AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930104 ) +AnnotationAssertion(rdfs:label obo:UBERON_8930104 "connective tissue sheath of hair follicle") +SubClassOf(obo:UBERON_8930104 obo:UBERON_0002384) +SubClassOf(obo:UBERON_8930104 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002073)) + + +) \ No newline at end of file diff --git a/src/templates/hra-intestine-liver-skin.template.tsv b/src/templates/hra-intestine-liver-skin.template.tsv index 343048270..ed7a7fd39 100644 --- a/src/templates/hra-intestine-liver-skin.template.tsv +++ b/src/templates/hra-intestine-liver-skin.template.tsv @@ -1,6 +1,6 @@ -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|https://purl.org/ccf/ASCTB-TEMP_free-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_omental-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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 \ No newline at end of file +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|https://purl.org/ccf/ASCTB-TEMP_free-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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|https://purl.org/ccf/ASCTB-TEMP_omental-coli|PMID:29218384|PMID:30324463 UBERON:0012419 UBERON:0011198 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 of hair follicle "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 \ No newline at end of file From 67e58308cc17303f5e8dc1dcf8ed580a0307e26c Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Mon, 6 Jul 2026 09:09:53 -0400 Subject: [PATCH 4/6] Update HRA intestine/liver/skin OWL serialization @dragon-ai-agent --- src/templates/hra-intestine-liver-skin.owl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/templates/hra-intestine-liver-skin.owl b/src/templates/hra-intestine-liver-skin.owl index c2754c43b..547f5e1eb 100644 --- a/src/templates/hra-intestine-liver-skin.owl +++ b/src/templates/hra-intestine-liver-skin.owl @@ -15,15 +15,15 @@ Declaration(Class(obo:UBERON_8930100)) Declaration(Class(obo:UBERON_8930101)) Declaration(Class(obo:UBERON_8930102)) Declaration(Class(obo:UBERON_8930104)) -Declaration(DataProperty(obo:BFO_0000050)) +Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(obo:RO_0002175)) Declaration(AnnotationProperty(terms:contributor)) Declaration(AnnotationProperty(terms:date)) Declaration(AnnotationProperty(oboInOwl:hasDbXref)) Declaration(AnnotationProperty(oboInOwl:inSubset)) -Declaration(Datatype(obo:UBERON_0002073)) -Declaration(Datatype(obo:UBERON_0011198)) +Declaration(Class(obo:UBERON_0002073)) +Declaration(Class(obo:UBERON_0011198)) @@ -41,7 +41,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930100 "Wikipedia:Taenia_coli AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930100 ) AnnotationAssertion(rdfs:label obo:UBERON_8930100 "free taenia coli") SubClassOf(obo:UBERON_8930100 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930100 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) +SubClassOf(obo:UBERON_8930100 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) # Class: obo:UBERON_8930101 (mesocolic taenia coli) @@ -53,7 +53,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930101 "Wikipedia:Taenia_coli AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930101 ) AnnotationAssertion(rdfs:label obo:UBERON_8930101 "mesocolic taenia coli") SubClassOf(obo:UBERON_8930101 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930101 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) +SubClassOf(obo:UBERON_8930101 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) # Class: obo:UBERON_8930102 (omental taenia coli) @@ -65,7 +65,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930102 "Wikipedia:Taenia_coli AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930102 ) AnnotationAssertion(rdfs:label obo:UBERON_8930102 "omental taenia coli") SubClassOf(obo:UBERON_8930102 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930102 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) +SubClassOf(obo:UBERON_8930102 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) # Class: obo:UBERON_8930104 (connective tissue sheath of hair follicle) @@ -77,7 +77,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930104 "Wikipedia:Hair_follic AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930104 ) AnnotationAssertion(rdfs:label obo:UBERON_8930104 "connective tissue sheath of hair follicle") SubClassOf(obo:UBERON_8930104 obo:UBERON_0002384) -SubClassOf(obo:UBERON_8930104 DataSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002073)) +SubClassOf(obo:UBERON_8930104 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002073)) ) \ No newline at end of file From e29097d7ace3b6465ba949bbf9ec9f0299875c50 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Tue, 7 Jul 2026 03:05:18 +0000 Subject: [PATCH 5/6] Merge hra-intestine-liver-skin.owl into uberon-edit.obo MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Merges the 4 new HRA terms (UBERON:8930100 free taenia coli, UBERON:8930101 mesocolic taenia coli, UBERON:8930102 omental taenia coli, UBERON:8930104 connective tissue sheath of hair follicle) from the ROBOT-generated template into the main edit file, and removes the now-redundant src/templates/hra-intestine-liver-skin.owl. Requested by @zhengj2007 in PR #3716. Signed-off-by: @dragon-ai-agent --- 🤖 **Generated by @dragon-ai-agent** - Model: `claude-opus-4-7` - Agent harness: claude-code - Triggered by: @zhengj2007 - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/28838034623) --- src/ontology/uberon-edit.obo | 48 +++++++++++++ src/templates/hra-intestine-liver-skin.owl | 83 ---------------------- 2 files changed, 48 insertions(+), 83 deletions(-) delete mode 100644 src/templates/hra-intestine-liver-skin.owl diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 240b86a5b..5756c75fc 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225242,6 +225242,54 @@ 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:8930100 +name: free taenia coli +def: "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." [https://purl.org/ccf/ASCTB-TEMP_free-coli, ISBN:978-1496398949, PMID:29218384, PMID:30324463] +subset: added_by_HRA +xref: Wikipedia:Taenia_coli +is_a: UBERON:0012419 ! taenia coli +relationship: part_of UBERON:0011198 ! muscle layer of large intestine +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: terms:contributor https://orcid.org/0000-0002-2999-0103 +property_value: terms:date "2026-05-25T00:00:00Z" xsd:dateTime + +[Term] +id: UBERON:8930101 +name: mesocolic taenia coli +def: "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." [https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli, ISBN:978-1496398949, PMID:29218384, PMID:30324463] +subset: added_by_HRA +xref: Wikipedia:Taenia_coli +is_a: UBERON:0012419 ! taenia coli +relationship: part_of UBERON:0011198 ! muscle layer of large intestine +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: terms:contributor https://orcid.org/0000-0002-2999-0103 +property_value: terms:date "2026-05-25T00:00:00Z" xsd:dateTime + +[Term] +id: UBERON:8930102 +name: omental taenia coli +def: "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." [https://purl.org/ccf/ASCTB-TEMP_omental-coli, ISBN:978-1496398949, PMID:29218384, PMID:30324463] +subset: added_by_HRA +xref: Wikipedia:Taenia_coli +is_a: UBERON:0012419 ! taenia coli +relationship: part_of UBERON:0011198 ! muscle layer of large intestine +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: terms:contributor https://orcid.org/0000-0002-2999-0103 +property_value: terms:date "2026-05-25T00:00:00Z" xsd:dateTime + +[Term] +id: UBERON:8930104 +name: connective tissue sheath of hair follicle +def: "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:2078047, PMID:23036740] +subset: added_by_HRA +xref: Wikipedia:Hair_follicle +is_a: UBERON:0002384 ! connective tissue +relationship: part_of UBERON:0002073 ! hair follicle +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: terms:contributor https://orcid.org/0000-0002-2999-0103 +property_value: terms:date "2026-05-25T00:00:00Z" xsd:dateTime + [Typedef] id: aboral_to name: aboral to diff --git a/src/templates/hra-intestine-liver-skin.owl b/src/templates/hra-intestine-liver-skin.owl deleted file mode 100644 index 547f5e1eb..000000000 --- a/src/templates/hra-intestine-liver-skin.owl +++ /dev/null @@ -1,83 +0,0 @@ -Prefix(obo:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(rdfs:=) -Prefix(terms:=) -Prefix(oboInOwl:=) - - -Ontology( -Declaration(Class(obo:UBERON_0002384)) -Declaration(Class(obo:UBERON_0012419)) -Declaration(Class(obo:UBERON_8930100)) -Declaration(Class(obo:UBERON_8930101)) -Declaration(Class(obo:UBERON_8930102)) -Declaration(Class(obo:UBERON_8930104)) -Declaration(ObjectProperty(obo:BFO_0000050)) -Declaration(AnnotationProperty(obo:IAO_0000115)) -Declaration(AnnotationProperty(obo:RO_0002175)) -Declaration(AnnotationProperty(terms:contributor)) -Declaration(AnnotationProperty(terms:date)) -Declaration(AnnotationProperty(oboInOwl:hasDbXref)) -Declaration(AnnotationProperty(oboInOwl:inSubset)) -Declaration(Class(obo:UBERON_0002073)) -Declaration(Class(obo:UBERON_0011198)) - - - -############################ -# Classes -############################ - -# Class: obo:UBERON_8930100 (free taenia coli) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_free-coli") obo:IAO_0000115 obo:UBERON_8930100 "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.") -AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930100 obo:NCBITaxon_9606) -AnnotationAssertion(terms:contributor obo:UBERON_8930100 ) -AnnotationAssertion(terms:date obo:UBERON_8930100 "2026-05-25T00:00:00Z"^^xsd:dateTime) -AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930100 "Wikipedia:Taenia_coli") -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930100 ) -AnnotationAssertion(rdfs:label obo:UBERON_8930100 "free taenia coli") -SubClassOf(obo:UBERON_8930100 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930100 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) - -# Class: obo:UBERON_8930101 (mesocolic taenia coli) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_mesocolic-coli") obo:IAO_0000115 obo:UBERON_8930101 "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.") -AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930101 obo:NCBITaxon_9606) -AnnotationAssertion(terms:contributor obo:UBERON_8930101 ) -AnnotationAssertion(terms:date obo:UBERON_8930101 "2026-05-25T00:00:00Z"^^xsd:dateTime) -AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930101 "Wikipedia:Taenia_coli") -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930101 ) -AnnotationAssertion(rdfs:label obo:UBERON_8930101 "mesocolic taenia coli") -SubClassOf(obo:UBERON_8930101 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930101 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) - -# Class: obo:UBERON_8930102 (omental taenia coli) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:978-1496398949") Annotation(oboInOwl:hasDbXref "PMID:29218384") Annotation(oboInOwl:hasDbXref "PMID:30324463") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_omental-coli") obo:IAO_0000115 obo:UBERON_8930102 "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.") -AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930102 obo:NCBITaxon_9606) -AnnotationAssertion(terms:contributor obo:UBERON_8930102 ) -AnnotationAssertion(terms:date obo:UBERON_8930102 "2026-05-25T00:00:00Z"^^xsd:dateTime) -AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930102 "Wikipedia:Taenia_coli") -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930102 ) -AnnotationAssertion(rdfs:label obo:UBERON_8930102 "omental taenia coli") -SubClassOf(obo:UBERON_8930102 obo:UBERON_0012419) -SubClassOf(obo:UBERON_8930102 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011198)) - -# Class: obo:UBERON_8930104 (connective tissue sheath of hair follicle) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:2078047") Annotation(oboInOwl:hasDbXref "PMID:23036740") Annotation(oboInOwl:hasDbXref "https://purl.org/ccf/ASCTB-TEMP_connective-tissue-sheath") obo:IAO_0000115 obo:UBERON_8930104 "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.") -AnnotationAssertion(obo:RO_0002175 obo:UBERON_8930104 obo:NCBITaxon_9606) -AnnotationAssertion(terms:contributor obo:UBERON_8930104 ) -AnnotationAssertion(terms:date obo:UBERON_8930104 "2026-05-25T00:00:00Z"^^xsd:dateTime) -AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_8930104 "Wikipedia:Hair_follicle") -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_8930104 ) -AnnotationAssertion(rdfs:label obo:UBERON_8930104 "connective tissue sheath of hair follicle") -SubClassOf(obo:UBERON_8930104 obo:UBERON_0002384) -SubClassOf(obo:UBERON_8930104 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002073)) - - -) \ No newline at end of file From 8c51771468a60df0bfec7b3437a424dab5264616 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 6 Jul 2026 16:04:44 +0100 Subject: [PATCH 6/6] 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-intestine-liver-skin-reports/candidates.tsv | 0 .../outputs}/hra-intestine-liver-skin-reports/errors.tsv | 0 .../outputs}/hra-intestine-liver-skin-reports/input.tsv | 0 .../hra-intestine-liver-skin-reports/name_corrections.tsv | 0 .../outputs}/hra-intestine-liver-skin-reports/out_of_scope.tsv | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename {src/templates => bulk_ntr_workflow/outputs}/hra-intestine-liver-skin-reports/candidates.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-intestine-liver-skin-reports/errors.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-intestine-liver-skin-reports/input.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-intestine-liver-skin-reports/name_corrections.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-intestine-liver-skin-reports/out_of_scope.tsv (100%) diff --git a/src/templates/hra-intestine-liver-skin-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/candidates.tsv similarity index 100% rename from src/templates/hra-intestine-liver-skin-reports/candidates.tsv rename to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/candidates.tsv diff --git a/src/templates/hra-intestine-liver-skin-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/errors.tsv similarity index 100% rename from src/templates/hra-intestine-liver-skin-reports/errors.tsv rename to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/errors.tsv diff --git a/src/templates/hra-intestine-liver-skin-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/input.tsv similarity index 100% rename from src/templates/hra-intestine-liver-skin-reports/input.tsv rename to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/input.tsv diff --git a/src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/name_corrections.tsv similarity index 100% rename from src/templates/hra-intestine-liver-skin-reports/name_corrections.tsv rename to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/name_corrections.tsv diff --git a/src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/out_of_scope.tsv similarity index 100% rename from src/templates/hra-intestine-liver-skin-reports/out_of_scope.tsv rename to bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/out_of_scope.tsv