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Add HRA eye NTR template: inner/outer cortex of lens #3713

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Add HRA eye NTR template: inner/outer cortex of lens #3713

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30 changes: 30 additions & 0 deletions bulk_ntr_workflow/outputs/definitions/input/uberon_0000389.json
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{
"group_name": "uberon_0000389",
"parent_id": "UBERON:0000389",
"parent_label": "",
"term_counts": {
"leaf": 2,
"group": 0
},
"note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
"terms": [
{
"ntr_id": "http://purl.obolibrary.org/obo/UBERON_9900001",
"label": "Inner cortex",
"term_type": "leaf",
"system": "default",
"is_a": "INFER:UBERON:0000389",
"part_of": "INFER:UBERON:0000389",
"def_xref": "https://purl.org/ccf/ASCTB-TEMP_inner-cortex"
},
{
"ntr_id": "http://purl.obolibrary.org/obo/UBERON_9900002",
"label": "Outer cortex",
"term_type": "leaf",
"system": "default",
"is_a": "INFER:UBERON:0000389",
"part_of": "INFER:UBERON:0000389",
"def_xref": "https://purl.org/ccf/ASCTB-TEMP_outer-cortex"
}
]
}
49 changes: 49 additions & 0 deletions bulk_ntr_workflow/outputs/definitions/uberon_0000389.json
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{
"definitions": {
"Inner cortex": "A zone of the lens cortex that is located internal to the outer cortex, composed of lens fiber cells that are older and more mature than those of the outer cortex. The inner cortex together with the outer cortex surrounds the lens nucleus and consists of concentrically arranged lens fiber cells.",
"Outer cortex": "A zone of the lens cortex that is the outermost layer of the cortex, composed of newly generated lens fiber cells that are added from the lens epithelium. The outer cortex is located external to the inner cortex and represents the most recently formed lens fiber cells."
},
"wikipedia_images": {},
"xrefs": {
"Inner cortex": "Wikipedia:Lens_(vertebrate_anatomy)",
"Outer cortex": "Wikipedia:Lens_(vertebrate_anatomy)"
},
"def_xrefs_to_add": {
"Inner cortex": "PMID:10550792|PMID:20171212",
"Outer cortex": "PMID:10550792|PMID:20171212"
},
"leaf_template_rows": {
"Inner cortex": {
"is_a": "UBERON:0034944",
"part_of": "UBERON:0000389"
},
"Outer cortex": {
"is_a": "UBERON:0034944",
"part_of": "UBERON:0000389"
}
},
"resolved_relationships": {
"Inner cortex": "part_of",
"Outer cortex": "part_of"
},
"resolved_parents": {
"Inner cortex": "UBERON:0000389",
"Outer cortex": "UBERON:0000389"
},
"confirmed_matches": [],
"possible_matches": [],
"out_of_scope": [],
"name_corrections": [
{
"label": "Inner cortex",
"suggested": "inner cortex of lens",
"reason": "The unqualified term 'Inner cortex' is highly ambiguous (could refer to cortex of brain, adrenal, kidney, etc.). Standard anatomical nomenclature requires specification of the organ. Keep 'Inner cortex' as a narrow synonym."
},
{
"label": "Outer cortex",
"suggested": "outer cortex of lens",
"reason": "The unqualified term 'Outer cortex' is highly ambiguous (could refer to cortex of brain, adrenal, kidney, etc.). Standard anatomical nomenclature requires specification of the organ. Keep 'Outer cortex' as a narrow synonym."
}
],
"unresolvable": []
}
2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/template_groups_initial.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=|
4 changes: 4 additions & 0 deletions bulk_ntr_workflow/outputs/template_initial.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_9900001 Inner cortex [PENDING] https://purl.org/ccf/ASCTB-TEMP_inner-cortex INFER:UBERON:0000389 INFER:UBERON:0000389 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
http://purl.obolibrary.org/obo/UBERON_9900002 Outer cortex [PENDING] https://purl.org/ccf/ASCTB-TEMP_outer-cortex INFER:UBERON:0000389 INFER:UBERON:0000389 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
3 changes: 3 additions & 0 deletions bulk_ntr_workflow/source_data/eye.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
eye,https://purl.org/ccf/ASCTB-TEMP_inner-cortex,Inner cortex,,,UBERON:0000389,lens cortex,
eye,https://purl.org/ccf/ASCTB-TEMP_outer-cortex,Outer cortex,,,UBERON:0000389,lens cortex,
1 change: 1 addition & 0 deletions src/ontology/uberon-edit.obo
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Expand Up @@ -57,6 +57,7 @@ treat-xrefs-as-is_a: VHOG
remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
import: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_eye.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_skeleton.owl
import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl
import: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl
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5 changes: 5 additions & 0 deletions src/ontology/uberon-odk.yaml
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Expand Up @@ -178,5 +178,10 @@ components:
use_template: true
templates:
- hra-skeleton.template.tsv
- filename: hra_eye.owl
use_template: true
templates:
- hra-eye.template.tsv

workflows:
- docs
1 change: 1 addition & 0 deletions src/templates/hra-eye-reports/candidates.tsv
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label as_iri uberon_id note
1 change: 1 addition & 0 deletions src/templates/hra-eye-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
3 changes: 3 additions & 0 deletions src/templates/hra-eye-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
eye https://purl.org/ccf/ASCTB-TEMP_inner-cortex Inner cortex UBERON:0000389 lens cortex leaf
eye https://purl.org/ccf/ASCTB-TEMP_outer-cortex Outer cortex UBERON:0000389 lens cortex leaf
3 changes: 3 additions & 0 deletions src/templates/hra-eye-reports/name_corrections.tsv
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source_label corrected_label reason
Inner cortex inner cortex of lens The unqualified term 'Inner cortex' is highly ambiguous (could refer to cortex of brain, adrenal, kidney, etc.). Standard anatomical nomenclature requires specification of the organ. Keep 'Inner cortex' as a narrow synonym.
Outer cortex outer cortex of lens The unqualified term 'Outer cortex' is highly ambiguous (could refer to cortex of brain, adrenal, kidney, etc.). Standard anatomical nomenclature requires specification of the organ. Keep 'Outer cortex' as a narrow synonym.
4 changes: 4 additions & 0 deletions src/templates/hra-eye.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_8930000 inner cortex of lens A zone of the lens cortex that is located internal to the outer cortex, composed of lens fiber cells that are older and more mature than those of the outer cortex. The inner cortex together with the outer cortex surrounds the lens nucleus and consists of concentrically arranged lens fiber cells. https://purl.org/ccf/ASCTB-TEMP_inner-cortex|PMID:10550792|PMID:20171212 UBERON:0034944 UBERON:0000389 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:Lens_(vertebrate_anatomy)
http://purl.obolibrary.org/obo/UBERON_8930001 outer cortex of lens A zone of the lens cortex that is the outermost layer of the cortex, composed of newly generated lens fiber cells that are added from the lens epithelium. The outer cortex is located external to the inner cortex and represents the most recently formed lens fiber cells. https://purl.org/ccf/ASCTB-TEMP_outer-cortex|PMID:10550792|PMID:20171212 UBERON:0034944 UBERON:0000389 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:Lens_(vertebrate_anatomy)
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