BridgeDb 2.3.7

This minor release adds PubMed and DOI as identifier sources.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>2.3.7</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.7'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.7"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.3.7'

BridgeDb 2.3.6

This minor release updated the URL link out pattern for Wikidata to use Scholia and adds the Complex Portal as new data source.

The below examples assume you need just org.bridgedb.bio, and you can use it as template and modify to add other modules.

For Maven:

<dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>2.3.6</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.6'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.6"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.3.6'

BridgeDb 2.3.5

This release updated URL link out patterns for a few databases (Reactome, Ensembl) and adds a few data sources for diseases.

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>2.3.5</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.5'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.5"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:2.3.5'

BridgeDb 2.3.4

Minor release that adds new a data source (VMH metabolite), backports the /xrefsBatch/ webservice API call, and fixes the miRBase Sequence link out.

BridgeDb 2.3.3

Major bugfix release for BridgeDb 2.3.2 where accidentally a problem sneaked in. Moreover, four webserver clients (CRONOS, Uniprot, PICR, and Synergizer) which seems to be broken for some time now (please let me know if you were using them) have now been removed, one had a security issue in one of its dependencies.

Binary releases and Maven instructions can be found here.

BridgeDb 2.3.2

Second minor release adding AOP-Wiki as data source, updates the regexp for DrugBank (add salt support), and now compiles the QC tool by default too.

Binary releases and Maven instructions can be found here.

BridgeDb 2.3.1

Very minor release adding rapeseed as a new species and IUPHAR's Guide to Pharmacology as data source.

BridgeDb 2.3.0

Major BridgeDb release, to be picked up by all downstream projects and users. The changes include an update for the PICR client, better documentation, updated Open PHACTS URIs, minor updates to various data sources, added "Brachypodium distachyon" as recognized species, removed Uniprot-SwissProt as data source (just use Uniprot-TrEMBL), and the URL of the webservice can now be changed from the command line.

BridgeDb 2.2.2

BridgeDb v2.2.2 is a minor bug fix release since v2.2.1.

Fixes:

• recognition of the new HMDB identifiers
• reduces the size of Ant-based distributions (with jars that support OSGi)
• fixed the MIRIAM urn for some UniProt identifiers

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'