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SciCrunch / NIF-Ontology

NIF Standard Ontologies (NIFSTD)
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pka, pkc, mapk synonym issues #17

Closed tgbugs closed 9 years ago

tgbugs commented 9 years ago

I think this is probably an issue in GO but PKA, PKC, and MAPK are all listed as synonyms on GO:0004674 "protein serine/threonine kinase activity" which is incorrect and their actual protein entities (families?) don't have them listed as abbrevs or syns. Leads to nasty results.

memartone commented 9 years ago

I looked it up in GO and I don’t see these as synonyms. They really couldn’t be as one is a molecule and one is a molecular function. Could this be coming from SciGraph?

On Sep 30, 2015, at 9:43 PM, Tom Gillespie notifications@github.com wrote:

I think this is probably an issue in GO but PKA, PKC, and MAPK are all listed as synonyms on GO:0004674 "protein serine/threonine kinase activity" which is incorrect and their actual protein entities (families?) don't have them listed as abbrevs or syns. Leads to nasty results.

— Reply to this email directly or view it on GitHub https://github.com/SciCrunch/NIF-Ontology/issues/17.

tgbugs commented 9 years ago

The issue appears in scigraph, see here. I'm trying to figure out which ontology that is being pulled in from.

tgbugs commented 9 years ago

Looks like these are coming from our (out of date) local copy of go.owl located here: http://ontology.neuinfo.org/NIF/BiomaterialEntities/go.owl

In the github version this issue has been fixed because I now import the latest version of go, but I haven't switched the ftp version over yet.