BridgeDb 2.2.1

BridgeDb v2.2.1 is a minor bug fix release since v2.2.0.

Fixes:

• IDMapperUniprot does not follow relative redirects
• org.bridgedb jars published in Maven Central

The release to Maven Central mean you do no longer need to compile BridgeDb or add a <repository> to use BridgeDb JARs as a binary dependencies. The Maven build system will take care of transitive dependencies (e.g. other parts of BridgeDb that is needed)

The below examples assume you need just org.bridgedb.bio, modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>2.2.1</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.2.1'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.2.1"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.2.1'

BridgeDb 2.2.0 released

Major BridgeDb release, to be picked up by all downstream projects and users. The changes include more liberal loading of Derby files, new data sources (EPA CompTox Dashboard, BRENDA Ligands, MetaboLights), updated link out patterns, and the QC tool reports more information, including the overall identifier and mapping counts. Furthermore, it includes a considerable amount of work by the Open PHACTS projects, as detailed in a few past internal releases.

BridgeDb 2.1.3 Open PHACTS internal release

Internal BridgeDB release for Open PHACTS 2.1

Also available from myGrid's Maven repository

BridgeDb 2.1.2 Open PHACTS internal release

Internal BridgeDB release for Open PHACTS 2.0.

Also available from myGrid's Maven repository

Build info: http://build.mygrid.org.uk/ci/view/OpenPHACTS/job/ops-BridgeDb/59/

BridgeDb 2.1.1 released

Minor release that adds ChEMBL and KNApSAcK as data sources, and adds name and synonym support for the Biomart driver.

BridgeDb 2.1.0 released

ChangeLog 2.1.0 (2015-08-06)

• Update SwissLipids, BRENDA and wikidata
• Update InChiKey to PRIMARY id
• Fix designations for KEGG Reactome and PubChem-bioassay
• Added the InChIKey as DataSource, allowing at some point WikiPathways to be searched on InChIKey
• Added SwissLipids
• Added more detail on how to get DataSource's
• Also compiles the BatchMapper now
• Added 'Plasmodium falciparum' to the Organism enumeration
• Added alternative methods that allow getting attributes not just from the data source of the Xref, but from any or all of the data sources in the BridgeDb mapping file
• Added the regular expression for the Wikidata identifier
• Added Wikidata as DataSource
• Preferably take the existing system code, removing use of deprecated methods
• Added an initial two upgrade notes for BridgeDb 2.0
• Made the method setStrictDataSourceChecking deprecated, indicating it is not regular API and will disappear
• Introduced a compatibility mode, allowing BridgeDb to silently ignore inconsistencies and contradictions in DataSource registrations, e.g. with old Derby files
• Added column headers and brief descriptions for datasources
• QC tool:
  • Now only shows the removed IDs when you run it with '-DshowRemovedIDs=true'
  • More detailed change report (number of new genes added and genes removed)
  • Use the same relative values as with file size changes: as change to the old number of identifiers
  • Also report the full name
  • Updated the QC tool to BridgeDb 2.0

BridgeDb 2.0.0 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