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 data sources easily.

What is a Web Service?

A web service is a standardized, platform-independent mechanism for machines to interact over the network. These days, many major biological databases publish their data with web service API:

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. Cytoscape supports many web services including:

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...


Tip: View the animation demo for importing networks from web services.

Example #1: Retrieving Protein-Protein Interaction Networks from IntAct


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.

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.


Network generated from Entrez Gene data: The network above is generated from interaction data matching the keyword human muscular dystrophy. Edge color represents data source type (BIND, BioGRID, or HPRD).

Note: since NCBI client extracts interaction data from a huge dataset, it takes a long time (30 seconds - 5 minutes, depends on machine specifications and network connection) to import large set of interactions.

Example #3: Retrieving Pathways and Networks from Pathway Commons

Then, follow the three-step process outlined below:


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:


Pathway Commons Options

You can configure access options from the Options tab. There are two retrieval options:

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:

Import Attributes from External Database

Some of the web service clients can import attributes from external databases. BioMart client is an example. You can install it from Plugin Manager.

Example 1: Import Additional ID Sets and Annotations from BioMart



Example 2: Import Annotations from NCBI Entrez Gene Database


NCBI Entrez Gene database () can be used as network data source and annotation repository. You can use NCBI web service client to import gene annotations from Entrez Gene.


Use Multiple Services in a Workflow

Web services are useful when you combine the result from multiple data sources.

Example: Import and Annotate Networks




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

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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