[BioC] BioPAX parsing

[Martin Preusse]

Hi Oliver,  

I think there is a lot interest in a bioconductor package!

Personally, I would like to read pathways stored in the BioPAX format into any kind of graph. It's a philosophical question if reactions should have nodes or should sit on the edges :) So far I have not used any R graph package. But I assume there are some very generic packages which are flexible enough to support both direct and bi-partite pathway structure. I used e.g. the JUNG graph API for JAVA extensively.

I'm not sure what you mean with RDF/OWL triples. For me BioPAX is only a format to store a pathway. And I would like to bring it back into its natural form: a network!

Do you have any code to test? I have used RJava before. All this RDF and XML file format stuff kind of puzzles me though … :)

Cheers
Martin



Am Freitag, 15. Juni 2012 um 18:32 schrieb 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 (mailto: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)
>