[DAS2] Ontology URIs (was RE: types.rnc)

Helt,Gregg Gregg_Helt at affymetrix.com
Wed Nov 8 19:54:14 UTC 2006

I'll talk to Suzi in her role as co-PI at NCBO (National Center for Biomedical Ontolgoy).  We may be able to quickly work out a URI syntax (even if implementation of what the URIs resolve to comes later).


> -----Original Message-----
> From: Andrew Dalke [mailto:dalke at dalkescientific.com]
> Sent: Tuesday, November 07, 2006 6:23 PM
> To: Ed
> Cc: Helt,Gregg
> Subject: Re: types.rnc
> Ed:
> > What bothers me is "still undecided".  That doesn't belong in a
> > "frozen" spec.  Though I have no idea what the correct text to put
> > here is.
> Take for example
> http://genome.cbs.dtu.dk:9000/das/secretomep/types
>      <TYPE id="NC-SECRETORY" method="SecretomeP-1.0"
>        category="protein sorting" description="Ab initio predictions of
> non-classical i.e. not signal peptide triggered protein secretion"
>        evidence="IEA"
> ontology="http://www.geneontology.org/GO.evidence.shtml">35138</TYPE>
> It uses an ontology URI to describe which ontology scheme is
> used to describe the "evidence" value.  In this case it means
> "Inferred from Electronic Annotation"
> There is no long-term/stable URL scheme for GO.  Do we
> make something up?  Do we say "use a URL" and leave it
> at that?  I'll go for the latter as every reasonable
> scheme should end up as a URL.
> Except for those which are annotated from multiple ontologies.
> 					Andrew
> 					dalke at dalkescientific.com

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