[DAS2] Ontologies in DAS/2

Lincoln Stein lstein at cshl.edu
Tue Feb 7 16:51:55 UTC 2006

Allen's ideas seem very sensible and easy to manage. We can already serve 
associations between genomic features and GO terms via properties, so the 
concerns expressed in the discussion section about the big GO API shouldn't 


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
> 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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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
SANDRA MICHELSEN, AT michelse at cshl.edu

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