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 * Enter a search term, such as BRCA1  * Enter one or more search terms, such as BRCA1

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 Protein-Protein Interaction Networks from IntAct

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

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

  • Enter one or more search terms, 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 Pathways and Networks from Pathway Commons

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

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

Then, follow the three-step process outlined below:

attachment:3_steps.png

  • 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.

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:

  • Simplified Binary Model: Retrieve a simplified binary network, as inferred from the original BioPAX representation. In this representation, nodes within a network refer to physical entities only, and edges refer to inferred interactions.
  • Full Model: Retrieve the full model, as stored in the original BioPAX representation. In this representation, nodes within a network can refer to physical entities and interactions.

By default, the simplified binary model is selected.

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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