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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

A recent redesign of the framework is at the following website

The results are monthly updated, and can be downloaded at

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.



On Jul 20, 2012, at 12:32 PM, Michel Dumontier wrote:

  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

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

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