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Re: NDF-RT and Canada

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Fri, 20 Sep 2013 10:17:17 -0700
Message-ID: <CALcEXf7kMz0ud4jzyHCx+FgjKATZcFwE_4M31j0p=6nt2cs5Mw@mail.gmail.com>
To: Marc Dumontier <marc@mdumontier.com>
Cc: HCLS <public-semweb-lifesci@w3.org>
Hi Marc,
  DrugBank offers mappings to DPD. you can access drugbank data in RDF with
Bio2RDF.

bio2rdf.org/datasets/drugbank - summary page
http://drugbank.bio2rdf.org/fct - faceted browser
http://drugbank.bio2rdf.org/sparql  - sparql endpoint
http://download.bio2rdf.org/current/drugbank/ - rdf files


bio2rdf's prefix for DPD is 'dpd'.  from the summary page, we see that
there are 989 references from drugbank to dpd. that's nowhere near
complete, but at least these are curated.

 to get the list of mappings

select distinct ?x ?xref
where {
  ?x <http://bio2rdf.org/drugbank_vocabulary:xref> ?xref
  FILTER regex(?xref,"dpd")
}

using the browser, you can search for fluoxetine and get to
http://drugbank.bio2rdf.org/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fdrugbank%3ADB00472

the link to dpd is http://bio2rdf.org/dpd:2242124

getting the dpd into bio2rdf is on my todo already.

m.




On Fri, Sep 20, 2013 at 7:11 AM, Marc Dumontier <marc@mdumontier.com> wrote:

> Hi
>
>
> Is anyone aware of any open work done on querying data out of NDF-RT, or
> some informative literature on anyone mapping Canadian drugs to it?
>
> I've been asked to match as many Canadian drugs from the Health Canada
> Drug Product Database (DPD) to equivalent formulations in the NDF-RT
>
> Once I have those mappings, I will need to query for the drug interactions
> within, and probably expose some of the other linkages, but the initial
> goal is is get the drug interactions.
>
> I've loaded the OWL release in Apache Jena with no problem, and started
> writing some very basic SPARQL queries. I will need help stepping them up :)
>
> Thanks
>  --
> Marc Dumontier
> 519-584-5601
> http://oscardevel.com/wordpress/
> http://www.oscarmcmaster.org
>
>


-- 
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Friday, 20 September 2013 17:18:08 UTC

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