Visualising all KEGG metabolism in Cytoscape

Question

[JRCX]

I would like to visualize all KEGG metabolic reactions (thinking of Cytoscape, but maybe you know of others?).

I am aware of KGML readers and parsers, but I would like to go over that layer of individual pathways and KOs. Basically, what I would like is to input the network created by this rest call

And visualize that, or part of that. Does anyone know of a way to parse a list of KEGG reactions into a format that would be possible to read in Cytoscape or other network visualisation software?

Thanks in advance!

Answer 1

[xanderpico]

Looking at the output you have already generated, I think you will need to make "reaction nodes" in addition to nodes representing molecules. You'll then need to parse reactants (R) and products (P) per reaction (X) from your current file into a two-column format that looks like this:

source        target
------        ------
R1             X1
R2             X1
X1             P1
X1             P2
etc...

You can then import this as a SIF file. Next you'll need a node attribute files like this:

node       type
----       ----
R1        molecule
P1        molecule
X1        reaction
etc...

Import this and then you'll be able to style the reaction nodes as tiny boxes distinct from your molecule nodes.

Of course, all of this is what is handled by the various KEGG apps you've decided not to use... so, it's a bit of work to manually replace these apps.

[JRCX]

Thank you!

But, isn't it possible to represent the network with the metabolites as nodes only, connected by the reactions as edges? I'm thinking the network will be too crowded with two types of nodes...