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RE: OMIM

From: Lin MD, Simon <LINMD.SIMON@mcrf.mfldclin.edu>
Date: Tue, 7 Aug 2012 17:06:05 +0000
To: Chris Mungall <cjmungall@lbl.gov>, Michel Dumontier <michel.dumontier@gmail.com>, "Tian Xia (isutian@gmail.com)" <isutian@gmail.com>
CC: HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>, Peter Robinson <peter.robinson@charite.de>
Message-ID: <A5BD550FC766564987DA2A59779890303DFCDE3A@MCL-EXMB02.mfldclin.org>
Hi Michael,

There is another resource that broadly defines the relationships between diseases and genes.

The paper was published in 2009
Annotating the human genome with Disease Ontology
  www.biomedcentral.com/1471-2164/10/S1/S6/<http://www.biomedcentral.com/1471-2164/10/S1/S6/>

A recent redesign of the framework is at the following website
http://doa.nubic.northwestern.edu/pages/search.php

The results are monthly updated, and can be downloaded at
http://doa.nubic.northwestern.edu/pages/download.php

It would be great to provide an RDF repository of this Disease Ontology annotation of the human genome.

Dr. Tian Xia implemented most of the redesign of the annotation. I am copying him also on this email.

Best,

Simon


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<http://dumontierlab.com/>


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Received on Tuesday, 7 August 2012 17:06:57 GMT

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