Hi all- Has anyone worked out the problem of getting appropriate graph objects for the KEGG pathways? I'd like to overlay gene expression data on specific hyperG over-represented KEGG pathways. The BioC books use the example of the IMCA but does not illustrate how to use this process generically on other KEGG pathways. The vignette for the graph package says that this problem was not solved as of 2006. I read on the mailing list that the cMAP package may be useful but this is also over 2 years old and I also read that it was not complete c.f. with the available data on the web. I found the PID on the Nature web site and downloaded an XML file but I don't see an easy way of mapping the proteins to ENTREZ IDs or similar atomic identifiers. Has anyone written any code to parse this? Thanks, Fraser [[alternative HTML version deleted]]