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Re: drug side effects

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Fri, 29 May 2009 07:29:35 -0400
Message-ID: <4A1FC71F.5020601@openlinksw.com>
To: Matthias Samwald <samwald@gmx.at>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>, Holger Stenzhorn <holger.stenzhorn@deri.org>
Matthias Samwald wrote:
> The conversion of SIDER to aTags is now available, see
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags/datasets
>
> A small excerpt of the aTags:
> http://hcls.deri.org/atag/data/SIDER_atags_excerpt.html
>
> The aTags re-use URIs from DBpedia, OBO disease ontology and OBO 
> symptom ontology. Most statements link a DBpedia URI (a drug) to an 
> OBO URI (a disease/symptom).
>
> As a simple example, the following query shows statements in SIDER 
> that deal with some kind of CNS disease:
>
> SELECT ?atag_content ?some_cns_disease
> WHERE {
>  ?atag sioc:content ?atag_content .
>  ?atag sioc:topic ?some_cns_disease .
>  ?some_cns_disease rdfs:subClassOf disease_ontology:DOID_331 .
>  }
> LIMIT 500
>
> Results: http://tinyurl.com/SIDER-about-CNS
>
> Some of the results look funny, for example, Memantine has 
> 'Alzheimer's' listed as a side-effect. However, Memantine is actually 
> used as a treatment for Alzheimer's. I have to look into that -- maybe 
> SIDER should just be seen as providing associations between drugs and 
> diseases/symptoms, without specifying whether they cause or cure the 
> disease? This is also the case with the TCM datasets that Jun 
> converted to RDF recently.
>
> Note that the SPARQL endpoint currently only contains a part of the 
> data, possibly the Virtuoso Sponger has problems with parsing large 
> RDFa files. Also note that others also have recently converted SIDER 
> into RDF as well (Anja Jentsch, Peter Ansell).
>
> Cheers,
> Matthias Samwald
>
> DERI Galway, Ireland
> http://deri.ie/
>
> Konrad Lorenz Institute for Evolution & Cognition Research, Austria
> http://kli.ac.at/
>
>
Matthias,

We'll take a look at what's happening with the RDFa cartridge. This 
should be a none issue re. using the Virtuoso Crawler + RDFa Sponger 
Cartridge to put the extracted triples in a designated Named Graph.

-- 


Regards,

Kingsley Idehen	      Weblog: http://www.openlinksw.com/blog/~kidehen
President & CEO 
OpenLink Software     Web: http://www.openlinksw.com
Received on Friday, 29 May 2009 11:30:12 GMT

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