obophenotype · zhengj2007 · May 25, 2026 · Jul 6, 2026 · Jul 6, 2026 · Jul 6, 2026
diff --git a/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/candidates.tsv
@@ -0,0 +1 @@
+label	as_iri	uberon_id	note
diff --git a/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/errors.tsv
@@ -0,0 +1 @@
+label	as_iri	issue_type	parent_id	parent_label	detail
diff --git a/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/input.tsv b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/outputs/hra-intestine-liver-skin-reports/out_of_scope.tsv b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/source_data/intestine-liver-skin.csv 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,
diff --git 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-groups.template.tsv 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.template.tsv 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|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
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		label as_iri issue_type parent_id parent_label detail
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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.
Original file line number	Diff line number	Diff line change
		@@ -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=\|