Cytoscape Wiki|
← Revision 1 as of 2008-03-07 15:41:11 →
Size: 1899
Comment:
|
Size: 3051
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| === Importing Networks from External Databases === | Cytoscape users can import networks and pathways directly from external databases. |
| Line 3: | Line 3: |
|
Cytoscape includes the ability to import networks and pathways directly from external databases. To get started, select: File → Import → Network from web services... [PICTURE GOES HERE] By default, Cytoscape provides direct access to the following external resources: |
By default, direct access to the following external resources is provided: |
| Line 14: | Line 8: |
| === Basic Usage === | === Getting Started === |
| Line 16: | Line 10: |
| Cytoscape includes four !CytoPanels: '''''Control Panel''''' on the left, '''''Tool Panel''''' on the bottom of ''Control Panel'', '''''Data Panel''''' on the bottom, and '''''Result Panel''''' on the right. By default, ''Control Panel'' and ''Data Panel'' will appear. ''Result Panel'' may appear, depending on the mix of Cytoscape plugins that you currently have installed. ''Tool Panel'' will appear when you select the following commands under the ''Layout'' menu: ''Rotate'', ''Scale'', and ''Align and Distribute''. | To get started, select: File → Import → Network from web services... |
| Line 18: | Line 12: |
| All panels can be shown or hidden using the View → Show/Hide functions. | attachment:file_import.png |
| Line 20: | Line 14: |
| attachment:cytopanel-menu-items_25.png | === Example #1: Retrieving Protein-Protein Interaction Networks from IntAct === |
| Line 22: | Line 16: |
| In addition, !CytoPanels can be floated or docked by selecting the icon at the top right corner of each !CytoPanel. The icon and tooltip will change based on the !CytoPanel state. If the !CytoPanel is docked, clicking on the icon will float the !CytoPanel, as indicated by the “Float Window” tooltip. Alternatively, if the !CytoPanel is floating, clicking on the icon will dock the !CytoPanel, as indicated by the “Dock Window” tooltip. |
* 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. |
| Line 24: | Line 21: |
| attachment:cytopanel-float-dock-icon.png |
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. === 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.
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...