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attachment:3_steps.png

Importing Networks from External Databases

Cytoscape users can import networks and pathways directly from external databases.

By default, direct access to the following external resources is provided:

Getting Started

To get started, select: File → Import → Network from web services...

attachment:file_import.png

Example #1: Retrieving Data from IntAct

  • Select: File → Import → Network from web services...

  • From the pull-down menu, select the IntAct Web Service Client.

  • Enter a search term, such as BRCA1
  • Click the Search button.

attachment:intact_import.png

After confirming the download of interaction data, the network of BRCA1 will be imported and visualized.

Example #2: Retrieving Data from Pathway Commons

  • Select: File → Import → Network from web services...

  • From the pull-down menu, select the Pathway Commons Service Client.

Then, follow the three-step process outlined below:

  • Step 1: Enter your search term; for example: BRCA1
  • Step 2: Select the protein or small molecule of interest. Full details regarding each molecule is shown in the bottom left panel.
  • Step 3: Download a specific pathway or interaction network.

attachment:3_steps.png

Cytoscape_User_Manual/ImportingNetworksFromWebServices (last edited 2010-07-28 03:24:29 by KeiichiroOno)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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