Plugin availability

Introduction

CyThesaurus is a Cytoscape plugin providing identifier mapping services based on various resources. Currently the plugin support ID mapping resources from delimited text, PGDB file and BioMart web service. This plugin utilized BridgeDb API.

Use Cases

5 related use cases have been identified on Bader Lab ID Mapping page. 2 of them are closely related to this project:

Supported ID Mapping Resources

File- based

RDB based

Web service based

Code Base

Currently the plugin is based on Cytoscape 2.6. Porting to Cytoscape 3.0 is in plan.

ID mapping service for other plugin

An inter-plugin communication module was developed to support CyThesaurus plugin providing ID mapping services to other plugins. A inter-plugin communication package cytoscape-plugins-comm was developed. ( cytoscape-plugins-comm.jar, javadoc, src). It is recommended that other plugins, who need to request ID mapping services from CyThesaurus, include the CyThesaurusService, which wraps up most of the supported ID mapping services from CyThesaurus.

Demo plugin to consume ID mapping services

CyCommands

The namespace is idmapping. Please try help idmapping in the command tool to list all supported commands.

Citing CyThesaurus

Please use the following citation when referring to CyThesaurus :

This is an open access publication. You can read it directly at biomed central: http://www.biomedcentral.com/1471-2105/11/5

CyThesaurus_Plugin (last edited 2011-03-29 16:03:58 by JianJiongGao)

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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