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* From the pull-down menu, select !Intact Web Service Client. * Enter a search term, such as BRCA1; and click Search. |
* From the pull-down menu, select the Int``Act Web Service Client. * Enter a search term, such as BRCA1 * Click the Search button. |
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| After confirming the download of interaction data, the network of BRCA1 will be imported and visualized. | |
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* 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 |
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.
attachment:3_steps.png