I have a set of some what related KEGG pathways (glycolysis and tca cycle for example). Are there any tools available that can merge these pathways (say if I give KGML files of these pathways as input) ?. I came across a few tools that can visualize and manipulate individual pathways, but couldn't find anything that can merge them.
Thank you in advance
Quick fix that I found:
Looks like VisANT merges pathway files. I tried uploading TCA cycle and Glycolysis pathway KGML files and VisANT somehow connects one to another
Bear in mind, however, that the KGML is generally of lower quality than the graphical representations (missing information, orphan nodes, etc).
edit: Another possibility is to translate the KGML to SBML with KEGGTranslator and then merge the models using e.g. SemanticSBML. You might want to go the route via SBML anyway because it is a standard open format and the software support is better than for the KGML.
"Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data".
There are a few plugins available for importing KGML files as cytoscape networks (e.g. look for kgmlreader, genoscape...).
So, the user can import a couple of kegg pathway as separate networks and then merge them with the "merge networks" tools.