Hi Paul and Fraser,

  Thanks for your comments and suggestion! I also believe that KEGG writes
lots of information in the PNG file, which cannot be parsed from KGML files.
I had heard in a conference sometime ago that in the coming version of KGML
this will change, but for now I am not aware of such an approach and would
be thankful if anybody could suggest a solution.

  Nice holidays,
David

2009/12/17 Fraser Sim <fjsim@buffalo.edu>

> Hi Paul,
>
> I believe that you're absolutely correct that the KGML does not contain all
> of the KEGG 'nodes' and some are hard coded into the PNG files. This would
> prevent any automated approach to adding them into your graph objects. I
> think the manual approach is the only one which will work in the this case.
> Hopefully, someone else has found an automated solution as I'd like to take
> advantage of the same for my own analyses.
>
> Cheers,
> Fraser
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Paul Shannon
> Sent: Thursday, December 17, 2009 1:37 PM
> To: bioc
> Subject: [BioC] KEGGgraph: any way to obtain 'outcome' nodes?
>
> I have been very happy with the KEGGgraph package, and the easy access to
> KEGG pathways -- rendered as bioc graphs -- it provides.
>
> But now, alas, I am getting greedy...
>
> Let me use the human apoptosis pathway as an example.  Take a look, please,
> at  http://www.genome.jp/kegg/pathway/hsa/hsa04210.html
>
> Many of the signaling paths terminate in biological outcomes, or in other
> pathways.  Dephosphorylation of Bad, for instance, leads to its activation,
> which leads to apoptosis; this state is displayed on the KEGG page as an
> unbordered text node labeled 'Apoptosis'.  On the other hand,
> phosphorylation inhibits BAD, and leads to an unbordered text node labeled
> 'Survival/.
>
> As best I can tell, the KEGG xml files do not mention these outcome nodes.
> Perhaps they only exist in hand curated form, in the png images displayed
> on
> the website.
>
> Before I manually add outcome nodes to my own curated and evolving version
> of the graphNEL produced by parseKGML2Graph, I want to ask: has this
> problem
> been faced by anyone else?  Does anyone have a procedure for creating
> graphNELs which capture all of the nodes and edges seen at
> http://www.genome.jp/kegg/pathway/hsa/hsa04210.html?
>
> Many thanks,
>
>  - Paul
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-- 
Jitao David Zhang
Biological Statistics and Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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