Opening Biogrid Files In Cytoscape

Question

[Michael Schubert]

I'm trying to visualize a Biogrid protein interactio network in Cytoscape.

However, Cytoscape does not recognize Biogrid's tab2 format. There should be a plugin to handle this type of conversion but it does not work with the current version of Cytoscape.

Do you have any ideas on conversion tools, workarounds, or a Cytoscape version in which the plugin does work?

Answer 1

[Michael Kuhn]

You could try to query Biogrid via Cytoscape's PSICQUIC plugin, which uses a standardized query interface:

[Michael Schubert]

Thanks, this works! :)

[boczniak767]

In fact, this method could find different number of interactions than saved in file downloaded from BioGrid website.

Answer 2

[Pierre Lindenbaum]

Try to use the PSI-MI XML format 2.5 instead of this tab2 format

[Michael Schubert]

I already tried importing that file format with Import>Network but it failed with a "could not open format" error.

Answer 3

[Wayne]

Ive found that if you install the old version of Cytoscape you can load a network from BioGrid and then save it as a Cytoscape session. Then open that file in Cytoscape 3. Process is very annoying.. I'm not sure why there isn't backward compatibility for these apps.