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 > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Biological Statistics and Computational Biology Ph.D. Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]