The NetworkMerge plugin allows you to merge networks in Cytoscape. From version 1.1, NetworkMerge uses id mapping from BridgeDb to merge networks from different sources.

The NetworkMerge plugin is available in the standard plugin repository of Cytoscape, and can be installed using the Cytoscape Plugin Manager.

See also this documentation:

• GSoC08 project on network merge and ID mapping:  http://www.cytoscape.org/cgi-bin/moin.cgi/Advanced_Network_Merge_and_ID_Mapping#API_Design
• GSoC08 ID mapping code:  http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/NetworkMerge/src/csplugins/id/mapping/

The source code of the NetworkMerge plugin for Cytoscape is available at:  http://chianti.ucsd.edu/svn/csplugins/trunk/soc/jgao/NetworkMerge