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...

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Example #1: Retrieving Protein-Protein Interaction Networks from IntAct

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

Tip: Expanding the Network: Several of the Cytoscape web services provide additional options in the node context menu. To access these options, right-click on a node and select "Use Web Services." For example, in the screenshot below, we have loaded the BRCA1 network from IntAct, and have chosen to merge this node's neighbors into the existing network.

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Example #2: Retrieving Pathways and Networks from Pathway Commons

Then, follow the three-step process outlined below:

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Downloading Pathways and Interaction Networks

In Step 3, you can simply double-click on a pathway of interest, or click on the Interaction Networks tab. The Interaction Networks tab enables you to filter interactions by data source and/or interaction type. For example, you can choose to restrict your network to direct physical interactions from HPRD and MINT only:

attachment:intxn_filter.png

Pathway Commons Options

You can configure access options from the Options tab. There are two retrieval options:

By default, the simplified binary model is selected.

Future Directions

As additional web service clients become available, they will be made available via the Cytoscape Plugin Manager. Once installed, these web service clients will be centrally accessible via the same steps defined above:

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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