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Re: Advancing translational research with the Semantic Web

From: <samwald@gmx.at>
Date: Thu, 17 May 2007 19:37:13 +0200
Message-ID: <20070517173713.260650@gmx.net>
To: public-semweb-lifesci@w3.org

> > <protein_a_expression_process> <has_participant> <protein_a> .
> > <protein_a_expression_process> <located_in> <tissue_b> .
> > <protein_a_expression_process> <described_by> <source_c> .
> The "protein expression process" class that needs to be introduced here 
> does seem a bit like bending over backwards 
> also you need to introduce
> an 
> additional predicate, "has_participant". This would certainly work,
> however 
> >from my point of view the best solution is the solution that uses the 
> fewest custom concepts, 

Hi Eric,

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.

Matthias Samwald


Yale Center for Medical Informatics, New Haven /
Section on Medical Expert and Knowledge-Based Systems, Vienna /

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Received on Thursday, 17 May 2007 17:37:28 UTC

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