Cytoscape Wiki|
Size: 862
Comment:
|
Size: 2783
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| 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 ==== |
| Line 9: | Line 16: |
| By default, Cytoscape provides direct access to the following external resources: | ==== Example #1: Retrieving Protein-Protein Interaction Networks from IntAct ==== |
| Line 11: | Line 18: |
|
* [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 a search term, such as BRCA1 * Click the Search button. |
| Line 14: | Line 23: |
| === Example #1: Retrieving Data from !IntAct === | attachment:intact_import.png |
| Line 16: | Line 25: |
| After confirming the download of interaction data, the network of BRCA1 will be imported and visualized. | |
| Line 17: | Line 27: |
| ==== Example #2: Retrieving Pathways and Networks from Pathway Commons ==== | |
| Line 18: | Line 29: |
|
* Select: File → Import → Network from web services... * From the pull-down menu, select the Pathway Commons Service Client. |
|
| Line 19: | Line 32: |
| === Example #2: Retrieving Data from Pathway Commons === |
Then, follow the three-step process outlined below: * 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. attachment:3_steps.png ===== 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 ===== Downloading 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. |
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 Service Client.
Then, follow the three-step process outlined below:
- 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.
attachment:3_steps.png
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
Downloading 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.