BridgeDb: BridgeDb v2.0.0 released

ChangeLog 2.0.0 (2014-11-21)

• Added the upcoming 10 alphanum ID format for Uniprot, see http://www.uniprot.org/docs/sp_soon.htm (2013-11-22)
• Added XMetDB (http://www.xmetdb.org/) as data source
• Removes redundant Sp code from build list
• Add Sugar Beet and Barley
• Added web service method to retrieve datasources.txt file
• Added ability to write a DataSource file in txt format
• Changed BioDataSource.init calls to DataSourceTxt.init() calls
• Split read funtionality out of Depricated BioDataSource
• UrnBased changed to mirianBase None miriam UrnBase no longer allowed Although call using syscode are ignored
• Added Identifiers.org methods to same information
• Stopped Unintended creation of Datasource with null sysCode.
• Added stricker methods to xref as well
• Stricketer builder where appropriate
• getUrl replaced with a safer methods
• Alernative name and description now saved to sysCode
• getByFullName and getBySystem code replaced with safer methods
• DataSource Registration now much Stricter. SysCode and fullName may not be null SysCode and fullName must be unigue. (or already paired)
• Added Oryza Indica as well as with the NCBI taxonomy terms
• Add a number of Miriam URN bases not yet in DataSource.txt
• Added 'Oryza sativa Japonica Group'
• updated Ensembl linkout pattern to support plants, fungi, and bacteria
• Support WP identifiers with revision supplement
• Read the regex patterns too
• Updated the Unigene website URL to remove the redirect step
• Fixed a race condition: initialization of Organism and BioDataSource depended on each other
• A method using deprecated data should be deprecated too
• Updated the MIRIAM urn for the Gene Ontology
• Added taxonomy support for Organism's
• Addressed some issues identified by Christian in the deprecated API
• Copied the Uniprot ID pattern from MIRIAM
• Include transient deps in the distribution
• Move OSGi bundles to transient