monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
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remove pseudo-blank nodes in OMIA #997

Open cmungall opened 3 years ago

cmungall commented 3 years ago
<https://monarchinitiative.org/MONARCH_b02402c255860259e85b> <http://purl.org/oban/association_has_object> <https://omia.org/OMIA001824-9913> .
<https://monarchinitiative.org/MONARCH_b02402c255860259e85b> <http://purl.org/oban/association_has_predicate> <http://purl.obolibrary.org/obo/RO_0002200> .
<https://monarchinitiative.org/MONARCH_b02402c255860259e85b> <http://purl.org/oban/association_has_subject> <https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> .
<https://monarchinitiative.org/MONARCH_b02402c255860259e85b> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/oban/association> .

=> some variant of SMC2 has-phenotype Haplotype HH3

(I don't think a haplotype is a phenotype but let's put that to the side or another ticket)

here is the pseudoblank:

<https://monarchinitiative.org/MONARCH_b02402c255860259e85b> <http://purl.org/oban/association_has_subject> <https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <http://purl.obolibrary.org/obo/GENO_0000408> <https://www.ncbi.nlm.nih.gov/gene/388275696> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <http://purl.obolibrary.org/obo/GENO_0000418> <https://www.ncbi.nlm.nih.gov/gene/388275696> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <http://purl.obolibrary.org/obo/RO_0002200> <https://omia.org/OMIA001824-9913> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <https://monarchinitiative.org/MONARCH_anonymous> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/GENO_0000512> .
<https://monarchinitiative.org/.well-known/genid/bd6bff744a66b4b1dd07> <http://www.w3.org/2000/01/rdf-schema#label> "some variant of SMC2" .

I think we want to directly link NCBIGene:388275696 to the 'phenotype' following biolink

Aside: we should not be using URLs like https://www.ncbi.nlm.nih.gov/gene/388275696 as our PURLs