Diff for "Cytoscape_User_Manual/ImportingNetworksFromWebServices"

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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

Example #2: Retrieving Data from Pathway Commons

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

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-Cytoscape includes the ability to import networks and pathways directly 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 ===
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-By default, Cytoscape provides direct access to the following external resources:
+=== Example #1:  Retrieving Data from IntAct ===
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- * [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.
+ * Select: File &rarr; Import &rarr; Network from web services...

 * 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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-=== Example #1:  Retrieving Data from !IntAct ===
+attachment:intact_import.png