Diff for "Cytoscape_User_Manual/ImportingNetworksFromWebServices"

Differences between revisions 13 and 25 (spanning 12 versions)

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 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.

Tip: Expanding the Network: Several of the Cytoscape web services provide additional options in the node context menu. To access these options, right-click on a node and select "Use Web Services." For example, in the screenshot below, we have loaded the BRCA1 network from IntAct, and have chosen to merge this node's neighbors into the existing network.

attachment:node_context2.png

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.

Future Directions

As additional web service clients become available, they will be made available via the Cytoscape Plugin Manager. Once installed, these web service clients will be centrally accessible via the same steps defined above:

File → Import → Network from web services...

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

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-=== Importing Networks from External Databases ===
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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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- * Enter a search term, such as BRCA1
+ * Enter one or more search terms, such as BRCA1
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-=== Example #2:  Retrieving Pathways and Networks from Pathway Commons ===
+'''Tip:  Expanding the Network:'''  Several of the Cytoscape web services provide additional options in the node context menu.  To access these options, right-click on a node and select "Use Web Services."  For example, in the screenshot below, we have loaded the BRCA1 network from !IntAct, and have chosen to merge this node's neighbors into the existing network.



attachment:node_context2.png



== 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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+Line 42:
-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:
+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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+Line 47:
+=== 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.



== Future Directions ==



As additional web service clients become available, they will be made available via the Cytoscape Plugin Manager.  Once installed, these web service clients will be centrally accessible via the same steps defined above:



 * File &rarr; Import &rarr; Network from web services...