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ncbo / BioPortal-to-KGX

Assemble a BioPortal Knowledge Graph
BSD 3-Clause "New" or "Revised" License
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UMLS semantic types not being applied #63

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Despite presence of attributes like hasSTY, nodes with corresponding semantic types are not being assigned the corresponding Biolink category. The STY ontology is being correctly mapped:

id      category        name    description     provided_by
STY:T058        biolink:Activity                        Semantic Types Ontology
STY:T057        biolink:Activity                        Semantic Types Ontology
STY:T056        biolink:Activity                        Semantic Types Ontology
STY:T055        biolink:Behavior                        Semantic Types Ontology
STY:T054        biolink:Behavior                        Semantic Types Ontology
STY:T053        biolink:Behavior                        Semantic Types Ontology
STY:T052        biolink:Activity                        Semantic Types Ontology

Yet these don't end up in the UMLS ontologies:

$ more MEDDRA_20_nodes.tsv 
id      category        name    description     provided_by
MEDDRA:10007469 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDDRA:10007467 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDDRA:10007468 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDDRA:10007465 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDDRA:10007466 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDDRA:10007463 biolink:OntologyClass                   Medical Dictionary for Regulatory Activities Terminology (MedDRA)
caufieldjh commented 2 years ago

This may be happening because append_new_types() assumes node IDs are not CURIEs, which is fine if we haven't done CURIE remapping, but it's more likely that we'll have them.