Improve filtering for gene product nodes in GPAD output

geneontology / minerva

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Improve filtering for gene product nodes in GPAD output #208

Open balhoff opened 5 years ago

balhoff commented 5 years ago

Currently certain IRI spaces are filtered out. This is prone to be incomplete. Need to improve NEO situation so that the correct nodes to be annotation subjects can be found semantically.

https://github.com/geneontology/minerva/blob/687a859b934888195497c126ab9e34f971e5ff3c/minerva-converter/src/main/resources/org/geneontology/minerva/legacy/sparql/gpad-basic.rq#L66-L72

goodb commented 5 years ago

Why do you have a biopax constraint in there? I don't think that is in anything I'm producing at this point.

balhoff commented 5 years ago

Why do you have a biopax constraint in there? I don't think that is in anything I'm producing at this point.

Probably from some earlier version of your stuff? But it ought to be harmless.

vanaukenk commented 3 years ago

@balhoff Is this still an issue for the GPAD output and can we close this ticket now? Thx.

balhoff commented 3 years ago

This is still an issue. Ideally query for the biolink category, which is in NEO as a triple like this:

<http://identifiers.org/wormbase/2L52.2> <https://w3id.org/biolink/vocab/category> <https://w3id.org/biolink/vocab/GeneProduct>

I don't know how easy these triples are to integrate into the model queries we do now.