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Re: seeks input on Study Data Exchange Standards

From: Kathrin Dentler <k.dentler@vu.nl>
Date: Wed, 22 Aug 2012 16:31:44 +0200
Message-ID: <5034ED50.10700@vu.nl>
To: <public-semweb-lifesci@w3.org>
Hi Peter,

It is also possible to store the transitive closure of SNOMED (which can 
be created by looping an SQL query until no new relations are inserted) 
in a relational database and query it with SQL. The following extract is 
a part of an SQL query that retrieves patients who had a colectomy or 
any subconcept of colectomy:

`colectomy`.`snomedctconceptid` = '23968004' OR EXISTS (SELECT * FROM 
`snomed`.`sct_transitiveclosure` AS tc WHERE `tc`.`SupertypeId` = 
'23968004' AND `tc`.`SubtypeId` = `colectomy`.`snomedctconceptid`)

You can find details in the "SNOMED Clinical Terms Transforming 
Expressions to Normal Forms" document.


>> ..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 Sent with Sparrow (http://www.sparrowmailapp.com)

Kathrin Dentler

AI Department         |   Department of Medical Informatics
Faculty of Sciences   |   Academic Medical Center
Vrije Universiteit    |   Universiteit van Amsterdam
k.dentler@vu.nl       |   k.dentler@amc.uva.nl
Received on Wednesday, 22 August 2012 14:32:16 UTC

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