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Re: NDF-RT and Canada

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Fri, 20 Sep 2013 13:46:22 -0700
Message-ID: <CALcEXf5PiMscmn2jh7JYbLb6kupd8nYsCuqTT7qhC1AUCeavBw@mail.gmail.com>
To: Marc Dumontier <marc@mdumontier.com>
Cc: HCLS <public-semweb-lifesci@w3.org>
Also, Rich Boyce has done some work [1] to map SPL to Bio2RDF and other
resources, and Chris Chute showed how to map to ndf-rt and rxnorm [2]

[1] http://www.ncbi.nlm.nih.gov/pubmed/23351881
[2] http://www.ncbi.nlm.nih.gov/pubmed/23256517

m.


On Fri, Sep 20, 2013 at 10:17 AM, 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
>



-- 
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 20:47:09 UTC

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