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| === Importing Networks from External Databases === | Cytoscape users can import networks and pathways directly from external databases. |
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| Cytoscape includes the ability to 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 Protein-Protein Interaction Networks 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 → Import → Network from web services... * From the pull-down menu, select the Int``Act Web Service Client. * Enter one or more search terms, such as BRCA1 * Click the Search button. |
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| === Example #1: Retrieving Data from !IntAct === | attachment:intact_import.png |
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| After confirming the download of interaction data, the network of BRCA1 will be imported and visualized. | |
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| attachment:tip.png ''' 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. | |
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| attachment:node_context2.png | |
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| === Example #2: Retrieving Data from Pathway Commons === |
== 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 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.
attachment:tip.png 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...