[BioC] DEGraph graph format?

[Oliver Ruebenacker]

     Hello Laurent,

  Thanks for the response. To my knowledge, Rredland is not maintained
any more. Since I am very familiar with Java (and OpenRDF Sesame), I
was thinking of using RJava to drive Sesame.

  Can you explain some more why you choose not to use Rredland? It
seems almost certainly relevant for the design of a BioPAX package.
Did the issue have to do with separating the actual reaction network
from other types of information?

  Thanks!

     Take care
     Oliver

On Sun, Jun 10, 2012 at 1:44 AM, laurent jacob <laurent.jacob at gmail.com> wrote:
> Hi Oliver,
>
> 2012/6/9 Oliver Ruebenacker <curoli at gmail.com>:
>>     Hello,
>>
>>  Does this package use a BioPAX parser that could be used for other
>> BioPAX data? Does it read level 2 or level 3 or both?
>>
>>  I'm looking for a BioPAX parser and would be willing to help build
>> one if none exists.
>
> I think Rredland
> (http://bioconductor.org/packages/2.4/bioc/html/Rredland.html) parses
> biopax in R.
>
> I didn't use it for this package because after that I also needed to
> convert the read structure to graphNEL objects, which was not
> straightforward. I read the biopax files in Cytoscape, then used
> RCytoscape (http://bioconductor.org/packages/release/bioc/html/RCytoscape.html)
> to read the networks built by Cytoscape.
>
> Best,
>
> Laurent
>
> --
> Laurent Jacob
> Department of Statistics
> UC Berkeley
> http://cbio.ensmp.fr/~ljacob



-- 
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)