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Re: One ontology schema - heterogeneous instance bases

From: Xiaoshu Wang <wangxiao@musc.edu>
Date: Sat, 08 Sep 2007 11:12:16 +0100
Message-ID: <46E27580.1020306@musc.edu>
To: Nigam Shah <nigam@stanford.edu>
CC: satya30@uga.edu, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org

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
Received on Saturday, 8 September 2007 10:13:05 GMT

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