FW: [BioPAX-discuss] Integrating BioPAX compliant data

From: Joanne Luciano <jluciano@genetics.med.harvard.edu> · Date: Fri, 10 Mar 2006 16:04:19 -0500

FYI...

>>The underlying data is stored in an RDF triple store

Joanne

-----Original Message-----
From: biopax-discuss-bounces@cbio.mskcc.org
[mailto:biopax-discuss-bounces@cbio.mskcc.org] On Behalf Of Nikesh Kotecha
Sent: Friday, March 10, 2006 2:36 PM
To: biopax-discuss@cbio.mskcc.org
Cc: Kyle Bruck; William Lu
Subject: [BioPAX-discuss] Integrating BioPAX compliant data

BioPAX community,

It is exciting to see the development of BioPAX and its support by major
pathway data sources.  Having data available in one format has definitely
helped with data integration.

As a proof of principle, we integrated human, ecoli and yeast pathway data
in BioPAX format from Kegg, BioCyc and Reactome.  It is available for
querying at http://pkb.stanford.edu.  The underlying data is stored in an
RDF triple store and all queries are made directly on the BioPAX model. This
has some drawbacks in terms of performance but has allowed us to preserve
the semantics specified in the BioPAX model.

We hope this is useful in continued development of the BioPAX standard.

Thank you,

Nikesh Kotecha
Kyle Bruck
William Lu

--
Nikesh Kotecha
Biomedical Informatics
Stanford University

Email: nikesh@stanford.edu
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