Diff for "Cytoscape_User_Manual/ImportingNetworksFromWebServices"

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:

• [http://www.ebi.ac.uk/intact/site/index.jsf IntAct]: an open source database of protein interaction data, hosted at EMBL-EBI.

• [http://www.pathwaycommons.org Pathway Commons]: an open source portal, providing access to multiple integrated data sets, including: Reactome, IntAct, HPRD, HumanCyc, MINT, the MSKCC Cancer Cell Map, and the NCI/Nature Pathway Interaction database.

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.