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

Chris Mungall cjm at fruitfly.org
Wed Nov 8 22:11:09 UTC 2006

There absolutely needs to be a stable URI scheme for referencing  
types defined in ontologies. The details of the scheme aren't clear  
yet. It will probably be http based (ie not LSID).

Do you have specific requirements? Should the URI be a URL  
dereferenceable in any browser? Should it dereference to html or RDF  
or use content negotion to decide which? etc

On Nov 8, 2006, at 2:54 PM, Helt,Gregg wrote:

> 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).
> 	gregg
>> -----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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