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

[Paul Shannon]

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