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 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 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 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)

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-=== Getting Started ===
+==== Getting Started ====
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-=== Example #1:  Retrieving Protein-Protein Interaction Networks from IntAct ===
+==== Example #1:  Retrieving Protein-Protein Interaction Networks from IntAct ====
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-=== Example #2:  Retrieving Pathways and Networks from Pathway Commons ===
+==== Example #2:  Retrieving Pathways and Networks from Pathway Commons ====
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- * From the pull-down menu, select the Pathway Commons Service Client.
+ * From the pull-down menu, select the Pathway Commons Web Service Client.
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+attachment:3_steps.png
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-attachment:3_steps.png
+===== Downloading Pathways and Interaction Networks =====
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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:
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-In Step 3, you can simply double-click on a pathway of interest, or click on the Interaction Networks tab.
+attachment:intxn_filter.png
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-The Interaction Networks tab enables you to filter interactions by data source and/or interaction type.
+===== Pathway Commons Options =====
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+Line 48:
-For example, you can choose to restrict your network to direct physical interactions from HPRD and MINT only.
+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.