Opening Biogrid Files In Cytoscape
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10.3 years ago

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?

cytoscape conversion • 3.9k views
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10.3 years ago

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

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Thanks, this works! :)

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

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10.3 years ago

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

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

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7.4 years ago
Wayne ★ 1.0k

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.

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