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openphacts / GLOBAL

Global project issues [private for now. owner lee harland]
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Justification for Ensembl Uniprot linksets #334

Open danidi opened 9 years ago

danidi commented 9 years ago

According to https://wiki.openphacts.org/index.php?title=IMS_2.0_reload#81:_Ensembl_to_Uniprot_.28Homo_Sapiens.2C_translation.29, the ensembl to uniprot linksets have the justification "gene". If it is connecting genes to proteins, I think proteinCodingGene would be more consistent with similar linksets. Might change regarding to decisions here https://github.com/openphacts/GLOBAL/issues/319.

AlasdairGray commented 9 years ago

Gene is certainly wrong here if it is connecting a gene with a protein. ProteinCodingGene is the recommendation for such linksets.

stain commented 9 years ago

Agreed, so justification should be http://semanticscience.org/resource/SIO_000985 then.

AlasdairGray commented 9 years ago

That's the URI listed in http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#appendix-link-justifications so yes

JonathanMELIUS commented 9 years ago

In my void header I already used the correct justification:

homo_sapiens-ensembl-uniprot-inferred_from_translation-linkset [...] bdb:linksetJustification sio:SIO_000985 ;

http://bridgedb.org/data/linksets/HomoSapiens/Ensembl_Hs_dataset.void.ttl

Chris-Evelo commented 8 years ago

Thanks Jonathan, I am really happy to see this kind of contributions.

Chris — Prof.Dr. Chris Evelo Dept. Head Bioinformatics – BiGCaT Maastricht University

From: JonathanMELIUS notifications@github.com<mailto:notifications@github.com> Reply-To: openphacts/GLOBAL reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday 3 December 2015 at 14:15 To: openphacts/GLOBAL GLOBAL@noreply.github.com<mailto:GLOBAL@noreply.github.com> Subject: Re: [GLOBAL] Justification for Ensembl Uniprot linksets (#334)

In my void header I already used the correct justification:

homo_sapiens-ensembl-uniprot-inferred_from_translation-linkset [...] bdb:linksetJustification sio:SIO_000985 ;

http://bridgedb.org/data/linksets/HomoSapiens/Ensembl_Hs_dataset.void.ttl

— Reply to this email directly or view it on GitHubhttps://github.com/openphacts/GLOBAL/issues/334#issuecomment-161635513.

stain commented 8 years ago

I double-checked our handling of this with @AlasdairGray and with regards to #334. We are OK with the bdb:linksetJustification - the reason ensembl transitives are not working now in the 2.0 IMS is that the link predicates like ensemblterms:DIRECT are not known to IMS - so it does not know if it's allowed to make new transitive relations.

The ensemblterm properties map to SKOS terms like skos:related - so I'll add to the IMS code to handle those properties as their equivalent skos properties.