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Re: NDF-RT and Canada

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Fri, 20 Sep 2013 13:12:26 -0700
Message-ID: <CALcEXf5LicNttqPhH0dsf2miicOmFZmVoFKjbAEpnENF4fMnHw@mail.gmail.com>
To: Mark <markw@illuminae.com>
Cc: Marc Dumontier <marc@mdumontier.com>, HCLS <public-semweb-lifesci@w3.org>
awwww thanks Mark !!!

m.


On Fri, Sep 20, 2013 at 12:22 PM, Mark <markw@illuminae.com> wrote:

> 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.
>



-- 
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 20:13:15 UTC

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