The way to use Omnipath in Cytoscape

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Jun 18, 2019, 1:18:26 PM6/18/19

to cytoscape-helpdesk

Using Omnipath, I got network.
However, there are only a few settings to download network.
Can I select target diseases and nodes?

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Jun 21, 2019, 11:43:23 AM6/21/19

to cytoscape-helpdesk

I forwarded your question to OmniPath's contact; hopefully they have answers for you.

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Jul 3, 2019, 2:37:00 PM7/3/19

to cytoscape-helpdesk

Hi,

OmniPath is a database compiled by the `pypath` Python module. We distribute it by the web service at http://omnipathdb.org/. The Cytoscape plug-in fetches the data from the web service, at the moment using only the `interactions` and the `ptms` queries.

`interactions` is a generic protein-protein and miRNA interaction network, it does not contain disease information.

In the web service you are able to limit the query to certain nodes, e.g. http://omnipathdb.org/interactions?partners=P00533,ULK1,ATG4B&genesymbols=1&fields=sources,references or http://omnipathdb.org/interactions?sources=MTOR&targets=ULK1&genesymbols=1&fields=sources,references&source_target=AND
In the Cytoscape plug-in we don't have option to select nodes prior to download, but afterwards you can use Cytoscape to select a subnetwork.

Best,

Denes

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