[DAS2] Ontologies in DAS/2

chris mungall cjm at fruitfly.org
Tue Feb 7 17:32:24 UTC 2006

What inferencing rules do you use for fetching features by their 

On Feb 7, 2006, at 8:51 AM, Lincoln Stein wrote:

> 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
> apply.
> 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
>> 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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