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| === Importing Networks from External Databases === |
== Web Service Client Manager == Cytoscape 2.6.0 has a new feature called '''Web Service Client Manager'''. This is a framework to manage various kinds of web service clients in Cytoscape. By using web service clients, users can access remote datasources easily. === What is a Web Service? === Web service is a standardized, platform-independent mechanism for machines to interact over the network. These days, many major biological databases publishes their system with web service API: |
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| Cytoscape includes the ability to import networks and pathways directly from external databases. |
* List of Biological Web Services: http://taverna.sourceforge.net/services * Web Services at the EBI: http://www.ebi.ac.uk/Tools/webservices/ This enables developers to write a program to access these services. Cytoscape core developer team have developed several sample web service clients using this framework. Currently, Cytoscape supports the following web services: * [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. * [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene NCBI Entrez Gene]: a public database of genes, including annotation, sequence and interactions. * [http://www.biomart.org/ Biomart]: an open source biological database engine. Useful for ID/Name mapping. All of these clients are available as Plugins and users can install them through Plugin Manager. In the following sections, users learn how to import network from extrenal databases. == Getting Started == |
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| [PICTURE GOES HERE] | attachment:file_import.png |
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| By default, Cytoscape provides direct access to the following external resources: | || '''Tip:''' View the [http://cbio.mskcc.org/~cerami/cytoscape/CytoWebServices.mov animation demo] for importing networks from web services. || |
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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. |
== Example #1: Retrieving Protein-Protein Interaction Networks from IntAct == |
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| === Basic Usage === |
* 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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| 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''. | attachment:intact_import.png |
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| All panels can be shown or hidden using the View → Show/Hide functions. | After confirming the download of interaction data, the network of BRCA1 will be imported and visualized. |
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| attachment:cytopanel-menu-items_25.png | ||<style="vertical-align: top; background-color: #CCCCCC;">''' 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 to the right, we have loaded the BRCA1 network from !IntAct, and have chosen to merge this node's neighbors into the existing network.||<style="background-color: #CCCCCC;"> attachment:node_context2.png|| |
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| 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. |
== Example #2: Retrieving Protein-Protein Interaction Networks from NCBI Entrez Gene == An entry of NCBI Entrez Gene has a section called ''Interactions''. NCBI web service client uses this section to build networks. |
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* Select: '''File → Import → Network from web services...''' * From the pull-down menu, select the '''NCBI Web Service Client'''. * Enter free-keywords. For example, type ''human muscular dystrophy''. * Click the Search button. attachment:entrez_import.png In this example, edge color represents a data source type. '''Note: since NCBI client extracts interaction data from a huge dataset, it takes a long time (30 sec. - 5 minutes, depends on machine spec. and network connection) to import large set of interactions. ''' == Example #3: 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... |
Web Service Client Manager
Cytoscape 2.6.0 has a new feature called Web Service Client Manager. This is a framework to manage various kinds of web service clients in Cytoscape. By using web service clients, users can access remote datasources easily.
What is a Web Service?
Web service is a standardized, platform-independent mechanism for machines to interact over the network. These days, many major biological databases publishes their system with web service API:
List of Biological Web Services: http://taverna.sourceforge.net/services
Web Services at the EBI: http://www.ebi.ac.uk/Tools/webservices/
This enables developers to write a program to access these services. Cytoscape core developer team have developed several sample web service clients using this framework. Currently, Cytoscape supports the following web services:
[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.
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene NCBI Entrez Gene]: a public database of genes, including annotation, sequence and interactions.
[http://www.biomart.org/ Biomart]: an open source biological database engine. Useful for ID/Name mapping.
All of these clients are available as Plugins and users can install them through Plugin Manager.
In the following sections, users learn how to import network from extrenal databases.
Getting Started
To get started, select: File → Import → Network from web services...
attachment:file_import.png
Tip: View the [http://cbio.mskcc.org/~cerami/cytoscape/CytoWebServices.mov animation demo] for importing networks from web services. |
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 to the right, 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 Protein-Protein Interaction Networks from NCBI Entrez Gene
An entry of NCBI Entrez Gene has a section called Interactions. NCBI web service client uses this section to build networks.
Select: File → Import → Network from web services...
From the pull-down menu, select the NCBI Web Service Client.
Enter free-keywords. For example, type human muscular dystrophy.
- Click the Search button.
attachment:entrez_import.png
In this example, edge color represents a data source type.
Note: since NCBI client extracts interaction data from a huge dataset, it takes a long time (30 sec. - 5 minutes, depends on machine spec. and network connection) to import large set of interactions.
Example #3: 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...