[BioC] KEGGgraph: any way to obtain 'outcome' nodes?

[Fraser Sim]

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 at stat.math.ethz.ch
[mailto:bioconductor-bounces at 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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