WIP: blml specification of gpi format (experimental)

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.
+