CyThesaurus_Plugin

Plugin availability

• From plugin manager: in category Network and Attribute I/O.

• Source code: http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/IDMapping/

• Tutorial: http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/ID_Mapping_Examples

• Release notes: http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin/Release

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:

• Unification during dataset merging: During a merge operation e.g. of two protein-protein interaction datasets from independently created databases, it is vital to recognize that two protein objects, one from each data source, represent the same protein molecule, even if the protein objects don’t share any database accession numbers. Unification requires knowledge of record type e.g. you cannot reliably use a gene ID to unify proteins (mostly because splice variants exist).

• Identifier translation: Some analysis methods require specific translations from one set of identifiers to another. For instance, our 'activity centers' analysis requires translation from protein or gene identifiers in a pathway database to Affymetrix probe set identifiers or other gene expression array platform identifiers.

Supported ID Mapping Resources

File- based

• Delimited text file

  • File format (e.g. http://tinyurl.com/mergesvn/testData/yeast_id_mapping.txt):

    • Each column for one ID type
    • Each row except the first one represents IDs of different types mapping to each other
    • First row contains ID types
    • Multiple IDs are allowed to be contained in one cell (One to many mapping, or IDs of the same type maps to each other). Use special character (e.g., ';', '/', etc, or user defined) to separate IDs.

RDB based

• PGDB file is supported

  • Gene database schema: http://www.bridgedb.org/wiki/GeneDatabaseLayout

  • Gene databases are available at http://bridgedb.org/data/gene_database/

Web service based

• BioMart web service has been utilized to provide ID mapping service in this plugin.

• BridgeDb web service is being developed.

• PICR - Protein Identifier Cross-Reference Service has been integrated.

• Synergizer web service has been integrated.

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

• A demo plugin, who consumes ID mapping services provided by CyThesaurus, is available for downloading (CyThesaurusServiceTester.jar).

• To run the demo plugin, install CyThesaurus plugin and place CyThesaurusServiceTester.jar in the plugin folder of Cytoscape, then start Cytoscape. You will see a menu of Test CyThesaurus Service in the Plugins menu. Click on the sub menus to request different services.

• To request ID mapping service example, you need to import the falFiltered.sif and load the BioMart ID Mapping Service with the dataset of Saccharomyces cerevisiae genes (SGD1.01). You can achieve this by going through Webservice-based identifier mapping tutorial.

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 :

• The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. BMC Bioinformatics. 2010 Jan 4;11(1):5.

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