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Add functional annotation extension for PDBe-KB integration #21

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Merged
cmungall merged 5 commits into from
Oct 29, 2025
Merged

Add functional annotation extension for PDBe-KB integration #21

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27f9857
Add comprehensive functional annotation extension for PDBe-KB integra…
claude Oct 17, 2025
2a89dd9
Fix validation issues in functional annotation examples
claude Oct 19, 2025
96c8512
Fix all validation issues in functional annotation examples
claude Oct 19, 2025
b308bae
Add comprehensive protein production and X-ray crystallography extens…
claude Oct 29, 2025
2bc155f
regenerated
claude Oct 29, 2025
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4,155 changes: 3,682 additions & 473 deletions assets/biostride.py
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757 changes: 755 additions & 2 deletions assets/graphql/biostride.graphql
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1,011 changes: 997 additions & 14 deletions assets/jsonld/biostride.context.jsonld
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12,227 changes: 9,545 additions & 2,682 deletions assets/jsonld/biostride.jsonld
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3,985 changes: 3,517 additions & 468 deletions assets/jsonschema/biostride.schema.json
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7,012 changes: 6,124 additions & 888 deletions assets/owl/biostride.owl.ttl
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42 changes: 41 additions & 1 deletion assets/prefixmap/biostride.yaml
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Expand Up @@ -3,12 +3,52 @@
"NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
"UBERON": "http://purl.obolibrary.org/obo/UBERON_",
"biostride": "https://w3id.org/biostride/",
"biostride_func": "https://w3id.org/biostride/functional-annotation/",
"biostride_schema": "https://w3id.org/biostride/schema/",
"dcterms": "http://purl.org/dc/terms/",
"linkml": "https://w3id.org/linkml/",
"nmdc": "https://w3id.org/nmdc/",
"prov": "http://www.w3.org/ns/prov#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"sio": "http://semanticscience.org/resource/",
"skos": "http://www.w3.org/2004/02/skos/core#"
"skos": "http://www.w3.org/2004/02/skos/core#",
"AggregatedProteinView": {
"@id": "biostride_func:AggregatedProteinView"
},
"BiophysicalProperty": {
"@id": "biostride_func:BiophysicalProperty"
},
"ConformationalEnsemble": {
"@id": "biostride_func:ConformationalEnsemble"
},
"ConformationalState": {
"@id": "biostride_func:ConformationalState"
},
"DatabaseCrossReference": {
"@id": "biostride_func:DatabaseCrossReference"
},
"EvolutionaryConservation": {
"@id": "biostride_func:EvolutionaryConservation"
},
"FunctionalSite": {
"@id": "biostride_func:FunctionalSite"
},
"LigandInteraction": {
"@id": "biostride_func:LigandInteraction"
},
"MutationEffect": {
"@id": "biostride_func:MutationEffect"
},
"PostTranslationalModification": {
"@id": "biostride_func:PostTranslationalModification"
},
"ProteinAnnotation": {
"@id": "biostride_func:ProteinAnnotation"
},
"ProteinProteinInteraction": {
"@id": "biostride_func:ProteinProteinInteraction"
},
"StructuralFeature": {
"@id": "biostride_func:StructuralFeature"
}
}
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