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Re: NDF-RT and Canada

From: Mark <markw@illuminae.com>
Date: Fri, 20 Sep 2013 21:22:06 +0200
To: Michel Dumontier <michel.dumontier@gmail.com>,Marc Dumontier <marc@mdumontier.com>
CC: HCLS <public-semweb-lifesci@w3.org>
Message-ID: <e72701d0-b9a4-4c3d-b8b9-9439a421ff04@email.android.com>
Michel, I love how comprehensive your responses are!  I always learn from them and I really should take a lesson from you in this regard vv my own projects!   :-)

M


Michel Dumontier <michel.dumontier@gmail.com> wrote:
>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

-- 
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Received on Friday, 20 September 2013 19:22:48 UTC

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