diff --git a/specs/gpi.yaml b/specs/gpi.yaml new file mode 100644 index 0000000..4085bbf --- /dev/null +++ b/specs/gpi.yaml @@ -0,0 +1,106 @@ +## IN PROGRESS + +prefixes: + biolink: 'https://w3id.org/biolink/vocab/' + biolinkml: 'https://w3id.org/biolink/biolinkml/' + gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md' + +classes: + gene product: + slots: + - id + - symbol + - name + - synonyms + - type + - taxon + - parent + - xrefs + - properties + + gene product properties: + slots: + - todo + +slots: + id: + identifier: true + required: true + mappings: + - biolink:id + - alliancegenome:primaryId + - gff3:ID + + symbol: + range: symbol type + multivalued: false + required: true + mappings: + - alliancegenome:symbol + - rdfs:label + + name: + range: string + multivalued: false + required: true + mappings: + - biolink:name + - gff3:Name + + synonyms: + range: string + multivalued: true + mappings: + - biolink:synonym + - alliancegenome:synonyms + - gff3:Alias + - skos:altLabel + + type: + range: category type + multivalued: false + required: true + mappings: + - biolink:type + - alliancegenome:soTermId + - gff3:type + - rdfs:type + + taxon: + range: taxon type + multivalued: false + required: true + mappings: + - alliancegenome:taxonId + - RO:0002162 + + parent: + range: gene product + multivalued: false ##? + mappings: + - gff3:Parent + + xrefs: + range: string + multivalued: true + mappings: + - alliancegenome:crossReferences # inlined + - gff3:Dbxref + +types: + symbol type: + pattern: "^\S+$" + base: str + uri: xsd:string + + category type: + typeof: uriorcurie + description: >- + A primitive type in which the value denotes a class within the biolink model. + + taxon type: + typeof: uriorcurie + pattern: "^NCBITaxon:\d+$" + description: >- + A primitive type in which the value denotes a class within the biolink model. +