[DAS2] Ontologies in DAS/2

[Lincoln Stein]

Hi,

I have group meeting from 12-1 every Tuesday, so I can't make this one. I'll 
be present for the telecon Wednesday at 12.

Lincoln


On Tuesday 07 February 2006 10:34, Helt,Gregg wrote:
> I talked to Suzi, she's planning to join our teleconference today to
> discuss ontologies, wearing her hat as co-PI of the National Center for
> Biomedical Ontology.  Hopefully Lincoln can join too.
>
> I took a closer look at the DAS/2 ontology work Allen has done (see
> http://biodas.org/documents/das2/das2_ontology.html).  I urge anyone who
> wants to contribute to the ontology discussion to read this doc.  It
> specifies a way to retrieve ontologies in OBOXML format.  In this format
> each ontology term gets an absolute URI through the same mechanism that
> the rest of DAS/2 uses (URIs for ids, which can be either absolute or
> relative but resolvable).  As Allen pointed out yesterday this would
> solve our problem of how to uniquely specify ontology terms in the DAS/2
> TYPES XML.
>
> I couldn't find any documentation for the OBOXML format, other than the
> code that generates it from OBO files.  But I'm using OBOXML as an
> example here because it clearly has resolvable URIs for each ontology
> term.  In Allen's spec, ontologies can also be returned in other
> formats, but it's unclear to me whether terms in these other formats
> would resolve to similar URIs.
>
> 	gregg
>
> > -----Original Message-----
> > From: das2-bounces at portal.open-bio.org
>
> [mailto:das2-bounces at portal.open-
>
> > bio.org] On Behalf Of Andrew Dalke
> > Sent: Tuesday, February 07, 2006 1:32 AM
> > To: DAS/2
> > Subject: Re: [DAS2] Notes from the DAS/2 teleconference for the code
> > sprint,6 Feb 2006
> >
> > > gh: would like a re-cast as xml document, hosted at so/sofa
> > > website. that xml would be like a std ontology representation so you
> > > could extend it. so someone could point to an extension of it.
> >
> > I asked as an action item if Gregg would look into the solution
> > for this.  Do we refer to the ontology by a "GO:0123456" identifier
> > or by some URL scheme?  If so, what's the mapping from URL scheme
> > to something that clients and people can understand, eg, to
> > ask for everything which is an exon?
> >
> > Does this mapping need a version number - does it change over time?
> >
> > 					Andrew
> > 					dalke at dalkescientific.com
> >
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>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724
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