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Re: OMIM

From: Chris Mungall <cjmungall@lbl.gov>
Date: Tue, 7 Aug 2012 09:46:20 -0700
Cc: HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>, Peter Robinson <peter.robinson@charite.de>
Message-Id: <398321B6-16C4-4D57-AE39-C0D05EAAAF27@lbl.gov>
To: Michel Dumontier <michel.dumontier@gmail.com>
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
> 
Received on Tuesday, 7 August 2012 16:49:34 GMT

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