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Re: seeks input on Study Data Exchange Standards

From: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Date: Wed, 22 Aug 2012 13:05:40 +0200
Message-ID: <533E5663310E487FA62829742993EEC0@zetsu>
To: <meadch@mail.nih.gov>, <Peter.Hendler@kp.org>
Cc: <kerstin.l.forsberg@gmail.com>, <public-semweb-lifesci@w3.org>
Peter wrote:
> Using both SQL and subsumption you can automatically find things like this: 
> "find all disorders that are a kind of adverse drug reaction where drug is a subtype of antibiotic and was given for a kind of gram negative bacterial infection of the digestive system". 

Simple subsumption such as that can be inferred by basic, RDFS-type reasoning. I don't see any potential problems caused by OWL's open world assumption here (please point them out if there are any).
Indeed, the open-world assumption of OWL can make creating expressive ontologies and using reasoners tricky. However, I do not see why the same should be true for using RDF, basic RDFS subsumptions and SPARQL. Could you provide some examples?

If we wanted to use more expressive ontologies with "intensional" entities (i.e., defined classes) in the overall system, we could simply run a reasoner and materialize the inferred statements for each ontology before it is 'shipped' for use by other systems. These other systems could then use simple RDF(S) and SPARQL (and maybe SPARQL rules), without the performance issues and potential unexpected consequences of open-world reasoning with expressive OWL ontologies. Specifying if and how exactly each specific node should be reasoned upon sounds so complex that I cannot imagine it working in any practical setting.

Best,
Matthias
Received on Wednesday, 22 August 2012 11:06:25 GMT

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