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geneontology / go-shapes

Schema for Gene Ontology Causal Activity Models defined using RDF Shapes
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Add has_primary_input/output to BP shapes? #283

Closed ukemi closed 3 months ago

ukemi commented 1 year ago

I just made a model for ascorbate biosynthesis for mouse and it is failing the ShEx. http://noctua.geneontology.org/editor/graph/gomodel:6348a65d00002622? Near as I can tell it is because it is failing the BP shape. Although I thought that the relations cascaded to subclasses, it looks like this isn't happening. Do we need to add the more specific input/output terms, to BP of maybe even to specific BPs like metabolic processes and transport?

vanaukenk commented 1 year ago

@ukemi Yes, we do need to add these.
This is listed as a task in the current Annotation Extensions project.

vanaukenk commented 1 year ago

Will add:

PREFIX GoMetabolicProcess: \http://purl.obolibrary.org/obo/GO_0008152 PREFIX GoTransport: \http://purl.obolibrary.org/obo/GO_0006810 PREFIX has_primary_input: \http://purl.obolibrary.org/obo/RO_0004009 PREFIX has_primary_output: \http://purl.obolibrary.org/obo/RO_0004008

\ @\ AND EXTRA a { a @\ {1}; has_primary_input: @\ ; has_primary_output: @\ ; } // rdfs:comment "a metabolic process GO biological process or child"

\ @\ AND EXTRA a { a @\ {1}; has_primary_input: ( @\ OR @\ OR @\ ) ; has_primary_output: ( @\ OR @\ OR @\ ) ; } // rdfs:comment "a transport GO biological process or child"

@ukemi