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Re: One ontology schema - heterogeneous instance bases

From: Gary Bader <bader@cbio.mskcc.org>
Date: Sun, 09 Sep 2007 12:29:35 -0400
Message-ID: <46E41F6F.9050806@cbio.mskcc.org>
To: wangxiao@musc.edu
CC: Nigam Shah <nigam@stanford.edu>, satya30@uga.edu, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org

	BioPAX is very active.  The proposal for the next level of BioPAX was 
sent out to the biopax-discuss mailing list last week and is open for 
discussion.  Please join the biopax-discuss list at 
biopax-discuss@biopax.org if you are interested.  The biopaxwiki.org 
wiki has current information about BioPAX.


Xiaoshu Wang wrote:
> Nigam Shah wrote:
>> Hi Satya,
>> See below...
>>> For example, the BioPAX ontology is a community effort to standardize
>>> the representation of pathway data. But, there are serious differences
>>> in the way concepts and relationships, defined in the BioPAX ontology
>>> schema, are interpreted to create instances. This leads to heterogeneous
>>> instance bases for the same ontology!
>> Well, BioPAX is an exchange format as of now. It gives you a 
>> consistent way of describing a pathway structure. It does not claim to 
>> provide a consistent terminology of pathway names that works across 
>> all sources.
> Using RDF as an "exchange format" is just outright wrong.  How do you 
> decide if an RDF document is in BioPAX format or not? I don't know how 
> active BioPAX is now (their website shows the last conference call was 
> more than two years ago). But such line of thought will doom (and have 
> perhaps already doomed) their fate.
> Xiaoshu

Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
Received on Sunday, 9 September 2007 16:31:44 UTC

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