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updating genome_annotation schema #192

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Merged
merged 24 commits into from
Aug 13, 2025
Merged

updating genome_annotation schema #192

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9aabdf4
updated modify_jsonldcontext to also change xref and iri to @type
puja-trivedi Jul 28, 2025
42ebd8f
updated comment in modify_jsonldcontext.py
puja-trivedi Jul 28, 2025
f88348e
added prefix for NCBIGene and NCBITaxon and removed ncbi prefix
puja-trivedi Jul 28, 2025
a54acd4
generate another formats for bke_taxonomy model(s)
Jul 28, 2025
f7a628f
removing NCBIGene prefix as it is already defined in bican_biolink
puja-trivedi Jul 28, 2025
60a8e27
Merge branch 'issue191' of https://github.com/puja-trivedi/models int…
puja-trivedi Jul 28, 2025
874960d
generate another formats for bke_taxonomy model(s)
Jul 28, 2025
53ef5f5
generate another formats for genome_annotation model(s)
Jul 28, 2025
420130f
updated NCBITaxon and NCBIAssembly prefix to the respective identifie…
puja-trivedi Jul 28, 2025
750395f
Merge branch 'issue191' of https://github.com/puja-trivedi/models int…
puja-trivedi Jul 28, 2025
49beaef
generate another formats for bke_taxonomy model(s)
Jul 28, 2025
f793823
Merge branch 'brain-bican:main' into issue191
puja-trivedi Jul 28, 2025
86f9756
generate another formats for genome_annotation model(s)
Jul 28, 2025
ce84ddf
reverted change to modify_jsonldcontext. iri and xref should not be s…
puja-trivedi Jul 29, 2025
6c52400
Merge branch 'issue191' of https://github.com/puja-trivedi/models int…
puja-trivedi Jul 29, 2025
5c607d5
generate another formats for bke_taxonomy model(s)
Jul 29, 2025
162897b
generate another formats for genome_annotation model(s)
Jul 29, 2025
19118cd
testing out change in linkml-runtime that automatically sets @type wh…
puja-trivedi Jul 30, 2025
4dde8dc
Merge branch 'issue191' of https://github.com/puja-trivedi/models int…
puja-trivedi Jul 30, 2025
5349d70
generate another formats for genome_annotation model(s)
Jul 30, 2025
55eda5b
generate another formats for bke_taxonomy model(s)
Jul 30, 2025
36790b1
removed modify_jsonldcontext.py because @type is now set by linkml-ru…
puja-trivedi Aug 13, 2025
0392f09
Merge branch 'issue191' of https://github.com/puja-trivedi/models int…
puja-trivedi Aug 13, 2025
d9a2f3a
Merge branch 'brain-bican:main' into issue191
puja-trivedi Aug 13, 2025
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13 changes: 7 additions & 6 deletions jsonld-context-autogen/bke_taxonomy.context.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -89,10 +89,7 @@
},
"NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
"NCBIGene": "http://identifiers.org/ncbigene/",
"NCBITaxon": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_",
"@prefix": true
},
"NCBITaxon": "http://identifiers.org/taxonomy/",
"NCIT": {
"@id": "http://purl.obolibrary.org/obo/NCIT_",
"@prefix": true
Expand Down Expand Up @@ -221,7 +218,10 @@
},
"@id": "authority"
},
"category": "@type",
"category": {
"@type": "xsd:anyURI",
"@id": "biolink:category"
},
"cell_type_set_type": {
"@id": "cell_type_set_type"
},
Expand Down Expand Up @@ -764,4 +764,5 @@
"@id": "VersionedNamedThing"
}
}
}
}

19 changes: 8 additions & 11 deletions jsonld-context-autogen/genome_annotation.context.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -88,12 +88,9 @@
"@prefix": true
},
"NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
"NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly/",
"NCBIAssembly": "http://identifiers.org/assembly/",
"NCBIGene": "http://identifiers.org/ncbigene/",
"NCBITaxon": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_",
"@prefix": true
},
"NCBITaxon": "http://identifiers.org/taxonomy/",
"NCIT": {
"@id": "http://purl.obolibrary.org/obo/NCIT_",
"@prefix": true
Expand Down Expand Up @@ -176,10 +173,6 @@
"gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#",
"gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#",
"linkml": "https://w3id.org/linkml/",
"ncbi": {
"@id": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=",
"@prefix": true
},
"oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
"orphanet": {
"@id": "http://www.orpha.net/ORDO/Orphanet_",
Expand Down Expand Up @@ -214,7 +207,10 @@
},
"@id": "authority"
},
"category": "@type",
"category": {
"@type": "xsd:anyURI",
"@id": "biolink:category"
},
"checksum_algorithm": {
"@context": {
"text": "skos:notation",
Expand Down Expand Up @@ -453,4 +449,5 @@
"@id": "VersionedNamedThing"
}
}
}
}

5 changes: 3 additions & 2 deletions linkml-schema/genome_annotation.yaml
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Expand Up @@ -8,8 +8,9 @@ prefixes:
linkml: https://w3id.org/linkml/
bican: https://identifiers.org/brain-bican/vocab/
schema: http://schema.org/
ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/
NCBIAssembly: http://identifiers.org/assembly/
NCBIGene: http://identifiers.org/ncbigene/
NCBITaxon: http://identifiers.org/taxonomy/

imports:
- linkml:types
Expand Down
8 changes: 5 additions & 3 deletions models_py-autogen/genome_annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,13 +71,15 @@ def __contains__(self, key:str) -> bool:
'imports': ['linkml:types', 'bican_biolink', 'bican_core'],
'name': 'genome-annotation-schema',
'prefixes': {'NCBIAssembly': {'prefix_prefix': 'NCBIAssembly',
'prefix_reference': 'https://www.ncbi.nlm.nih.gov/assembly/'},
'prefix_reference': 'http://identifiers.org/assembly/'},
'NCBIGene': {'prefix_prefix': 'NCBIGene',
'prefix_reference': 'http://identifiers.org/ncbigene/'},
'NCBITaxon': {'prefix_prefix': 'NCBITaxon',
'prefix_reference': 'http://identifiers.org/taxonomy/'},
'bican': {'prefix_prefix': 'bican',
'prefix_reference': 'https://identifiers.org/brain-bican/vocab/'},
'linkml': {'prefix_prefix': 'linkml',
'prefix_reference': 'https://w3id.org/linkml/'},
'ncbi': {'prefix_prefix': 'ncbi',
'prefix_reference': 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id='},
'schema': {'prefix_prefix': 'schema',
'prefix_reference': 'http://schema.org/'}},
'source_file': 'genome_annotation.yaml',
Expand Down
32 changes: 0 additions & 32 deletions utils/modify_jsonldcontext.py
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