[DAS2] Ontologies in DAS/2

Helt,Gregg Gregg_Helt at affymetrix.com
Tue Feb 7 15:34:21 UTC 2006

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.


> -----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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