Merging Kegg Pathways

Question

[Sudeep]

Dear All, 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

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edit:

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

Answer 1

[Michael Schubert]

KeggConverter can do this, for instance.

Bear in mind, however, that the KGML is generally of lower quality than the graphical representations (missing information, orphan nodes, etc).

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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.

[Sudeep]

Thank you ... but the link in the paper to the download page appears to be dead. I found this pathvisio project (http://www.pathvisio.org/wiki/KeggConverter) with same name but I am not sure if it is the same one.

[Michael Schubert]

You are right. The converter in PathVisio seems to just do KGML->GPML. I updated the answer.

Answer 2

[kandoigaurav]

A pretty old post, but thought it might help the future users. I wrote this little R script using KEGGgraph, tkWidgets and some base R graph functions.

library(tkWidgets)
library(KEGGgraph)
library(KEGG.db)

pathways = list.files(pattern="*.xml")
for (i in 1:length(pathways)) assign(pathways[i], parseKGML2Graph(pathways[i],expandGenes=TRUE))
rm(i);rm(pathways)
pathways<-objNameToList(objects(), parent.frame())
merged <- ugraph(mergeKEGGgraphs(pathways, edgemode = "directed"))

This will give you an undirected graph (because of ugraph() ). If you wish to retain the original directed graph, just replace the last line with the following:

merged <- mergeKEGGgraphs(pathways, edgemode = "directed")

Hope that helps!

[urwa]

Thanks a bunch. That was all I was looking for. I had one trouble though. My global environment has a lot of other values and datasets. So this command pathways<-objNameToList(objects(), parent.frame()) those other files. I have clear global environment before running the above code snippet. I am new with R so help would be appreciated.

Answer 3

[ff.cc.cc]

"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.

Good luck!

[Sudeep]

Thank you for your suggestion