importing large PPI databases in Cytoscape

Question

[Francois Piumi]

Hi,

I'd like to study all the interactions between a set of genes and a whole PPIs database (i.e. STRING, Biogrid or Intact) in Cytoscape.

A few years ago, I was able to import the full Intact PPIs database (file "taxidA_960_xgmml_cytoscape.xml", size approx 1 Go) but sometimes cytoscape crashed.

Now I'd like to import in Cytoscape the new version of the Intact database. The first problem is that it comes into several .xml files instead of one. EBI said that I had to import manually the 260 files in cytoscape and merge them.... :(

Then I tried to import other databases such as Biogrid, Genemania and STRING but Cytoscape doesn't support the import. I can see a kind of network with only some nodes (?)

So is it possible to import a full PPIs database ins Cytoscape ? If yes, what database could you import ?

Thanks

Francois

Answer 1

[xanderpico]

I would recommend browsing NDEx. This is a database by the Cytoscape team that already did all of the work of importing and converting, etc from major databases including Biogrid and STRING.

For STRING and GeneMANIA, there are dedicated Cytoscape apps that you should install and use.