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Re: OMIM

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Tue, 7 Aug 2012 13:51:36 -0400
Message-ID: <CALcEXf6h5ttVWMxfeOu5YBtvEROfFX0GawzYEN5Fh1FZdOVF8Q@mail.gmail.com>
To: Chris Mungall <cjmungall@lbl.gov>
Cc: HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>, Peter Robinson <peter.robinson@charite.de>
Hi Chris,
 We'll be moving the new omim build to the bio2rdf server (along with new
builds for pharmgkb, ncbi gene, CTD, drugbank, and a few others).  I've put
the store back up for now.

There are associations to HPO already in omim.  For instance:

http://bio2rdf.semanticscience.org:8009/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fomim_resource%3A261900_cs

Best,

m.

On Tue, Aug 7, 2012 at 12:46 PM, Chris Mungall <cjmungall@lbl.gov> wrote:

> Hi Michael
>
> I can't seem to connect to the triplestore.
>
> Have you considered adding associations between OMIM and phenotype
> ontology classes? These can be downloaded from
> http://www.human-phenotype-ontology.org/ as tab delimited files that can
> trivially be converted to an rdf model of choice (we will be providing OWL
> for this ourselves in the future, it will likely differ in modeling and
> URIs from bio2rdf).
>
> On Jul 20, 2012, at 12:32 PM, Michel Dumontier wrote:
>
> Hi,
>   Using the OMIM API [1], I produced an RDF version of OMIM (github code
> [2]) which I've subsequently loaded into a (temporary) virtuoso endpoint
> [3].  The easiest way to get into the system is through a faceted search
> [4], or from the list of types [5], or you can try looking at a VKORC1
> associated variation as an entry point [6].
>
> comments and suggestions welcome.
>
> [1]  http://www.omim.org/help/api
> [2]  https://github.com/bio2rdf/bio2rdf-scripts/blob/master/omim/omim.php
> [3]  http://bio2rdf.semanticscience.org:8009/sparql
> [4]  http://bio2rdf.semanticscience.org:8009/fct
> [5]  http://goo.gl/HQ8rO
> [6]
> http://bio2rdf.semanticscience.org:8009/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fomim_resource%3A608547_allele_1
>
>
> --
> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
> http://dumontierlab.com
>
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Tuesday, 7 August 2012 17:52:25 GMT

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