W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2012

Re: seeks input on Study Data Exchange Standards

From: Chime Ogbuji <chimezie@gmail.com>
Date: Wed, 22 Aug 2012 10:14:46 -0400
To: Peter.Hendler@kp.org
Cc: matthias.samwald@meduniwien.ac.at, kerstin.l.forsberg@gmail.com, meadch@mail.nih.gov, public-semweb-lifesci@w3.org
Message-ID: <E1D1C80C69314144997F7D72B2C1E497@gmail.com>
On Wednesday, August 22, 2012 at 10:04 AM, Peter.Hendler@kp.org wrote:
> ..snip..
> You mentions something I wonder about. If you lock the ontology (for example this is a release of SNOMED and you cant add new terms), and you run the reasoner and store all the inferred triplets as RDF along with all the stated ones, then could you really do just SPARQL at that point and not need a reasoner?

Yes, you can.  In using SPARQL to query such data you can either rely on 'reasoning' at the point of evaluating the query (in which case the dataset doesn't change) or 'directly' evaluating a query over the a priori deductions from reasoning and the original stated facts.  What you are describing is the latter strategy and of course introduces issues with synchronizing these additions with a) new data or b) updates to the ontology or rules.  Each approach has its strength and weaknesses, especially when considering use with clinical data that may be serving multiple purposes.
 
-- 
Chime Ogbuji
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> "Matthias Samwald" <matthias.samwald@meduniwien.ac.at (mailto:matthias.samwald@meduniwien.ac.at)> 
> 08/22/2012 04:05 AM 
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> To
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> <meadch@mail.nih.gov (mailto:meadch@mail.nih.gov)>, Peter Hendler/CA/KAIPERM@KAIPERM 
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> cc
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> <kerstin.l.forsberg@gmail.com (mailto:kerstin.l.forsberg@gmail.com)>, <public-semweb-lifesci@w3.org (mailto:public-semweb-lifesci@w3.org)> 
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> Subject
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> Re: seeks input on Study Data Exchange Standards
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> 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". 
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> 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? 
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> 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. 
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> Best, 
> Matthias 
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> 
Received on Wednesday, 22 August 2012 14:15:20 GMT

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