CyThesaurs Release Notes

Version 1.31

• Remove ID mapping resources from session file, use global props only

Version 1.30

• Fixed various bugs

• Updated to latest BridgeDb

Version 1.20

• Support CyCommands with namespace idmapping.

Version 1.11

• Support Cytoscape 2.7

Version 1.10

• Update BridgeDb.jar to 1.0

• Support BridgeDb web service

• Support CRONOS web service
• Type guessing

Version 1.04

• Handle the problem when failed to connect to BioMart.

• Give a list of base URLs of BioMarts.

Version 1.03

• Support mapping from non-identifier attribute such as symbols to identifiers.

Version 1.02

• Integrate AttributeMapper: now support mapping to Symbols if available.

• Support .bridge file.

• Bugfix: remember the previous selection.

Version 1.01

• Updating bridgedb.jar to incorporate bug fixes for IDMapperBiomart.

Version 1.0

• CyThesaurus is a plugin for performing ID mapping/translation for Cytoscape networks. In this version, the plugin supports translating node attributes in networks from source ID types to the target ID types and save the translated IDs in new attributes. The plugin utilized a ID mapping Java API package, called BridgeDb. It supports mapping IDs using different resources including text files, .pgdb Derby embeded files, and several web services, such as BioMart, PICR and Synergizer.

• CyThesaurus plugin also provides ID mapping services for other Cytoscape plugins. To consume the services, you can simply include the CyThesaurusService package in your plugin project and call methods in the CyThesaurusServiceClient.

• It is worth mentioning that a package supporting inter-plugin communication in Cytoscape 2.6.x was developed in the project. To support communication between plugins, you can include the cytoscape-plugins-comm package in your plugins and then passing messages among them. The source code and Java doc for the package is also available.