[BioC] BioPAX parsing

[Oliver Ruebenacker]

     Hello Martin,

  I'm currently looking into reading BioPAX into R using RJava and
OpenRDF Sesame. If there is interest, I may be looking into submitting
a package to BioConductor.

  It would be very helpful if you could tell me what you need the
BioPAX data for, and in what form it would be best for you. Possible
options are:

  - A data frame of the RDF/OWL triples
  - A graph of the RDF/OWL triples
  - A data frame with one row for each reaction-participant
  - A bi-partite graph with nodes for reactions and nodes for substances
  - A with nodes for substances only, with edges for interactions
  - A genetic interaction graph

  This list is roughly sorted form the one most easy to the most
difficult to provide.

     Take care
     Oliver

On Thu, Jun 14, 2012 at 10:01 AM, Martin Preusse
<martin.preusse at googlemail.com> wrote:
> Many biological pathway resourced provide their data in the BioPAX format (http://www.biopax.org/index.php), a special XML format for biological interaction networks. Examples are pathway commons (http://www.pathwaycommons.org/pc/) and Reactome (http://www.reactome.org (http://www.reactome.org/)).
>
> A JAVA library for parsing BioPAX files exists: http://www.biopax.org/paxtools.php
>
> Has anybody used BioPAX files with R? Is it possible to read BioPAX files in any R based graph structure? A solution similar to the KEGGgraph package for KEGG pahways would be great, since more and more databases start using BioPAX.
>
>
> Any ideas are appreciated!
>
> Cheers
> Martin
>
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-- 
Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)