Hi. I'm trying to create a network that will present all the pathways found in the KEGG database and the relations between those pathways. I want to represent each pathway as node, and compounds that are shared by two (or more...) pathways as edges. I have not found a tool to perform this task yet. I would be happy to get your advice on this issue. Thanks!
This is a common question around here. You didn't give us much information to go on so it's hard to make a clear suggestion, but for my own KEGG data I'm quite happy using Cytoscape and also have recently been communicating networks using hive plots.
I have a followup question, I want to identify incoming and outgoing edges for eg. http://www.kegg.jp/kegg-bin/show_pathway?hsa00010 to Pentose phosphate pathway (PPP) edge 1 (outgoing) from PPP edge 3 (incoming) citrate cycle 1, 1 (out and incoming) proponate metabolism 1 (out) carbon fixation 1 (in) starch and sucrose 1,1 (in, out)
How can I extract this from .xml or from any file? I can access all kegg file.