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Re: Advancing translational research with the Semantic Web

From: Eric Jain <Eric.Jain@isb-sib.ch>
Date: Fri, 18 May 2007 00:34:17 +0200
Message-ID: <464CD869.9060609@isb-sib.ch>
To: public-semweb-lifesci@w3.org

samwald@gmx.at wrote:
> The choice of this design pattern is not arbitrary, it is based on the
> OBO Relation Ontology [1], BFO and the OWL version of the Gene Ontoloy,
> which are becoming widely accepted. Other foundational ontologies (like
> DOLCE) have similar relations and entities. In other words: I have not
> introduced this design pattern to conform to my suggested approach. A
> well-designed ontology would use such classes and relations right from
> the start. Using such a design pattern increases opportunities for
> interoperability between ontologies significantly.

There does indeed seem to be an existing has_participant predicate, but is 
there also a "protein expression process" class? This would seem rather 
contrived, from a biologists (if not an ontologists) point of view (all we 
want to say, after all, is that the protein can be found in some tissue)!

Using widely used concepts and predicates is no doubt a good thing. But if 
you can instead make do with core RDF features, that's even better -- not 
everyone uses OBO, no matter how "foundational" it may be :-)

Note that the reification "design pattern" allows you to add attribution 
information on statements that you did not at first think would ever need 
such information, without breaking the data model.
Received on Thursday, 17 May 2007 22:36:10 UTC

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