BridgeDb 3.1.2 (Java 8)

This release is a Java8-compatible version of BridgeDb 3.1.2.

BridgeDb 3.1.2

This update release brings in BridgeDb Datasources 20240725, a new organism (Solanum tuberosum), and various small stability improvements. It includes the fix for the instantiation of Ensembl identifiers from their Bioregistry compact identifiers.

Full Changelog: release_3.1.1...release_3.1.2

BridgeDb 3.0.27

This update release brings in BridgeDb Datasources 20240725, a new organism (Solanum tuberosum), and various small stability improvements.

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>3.0.27</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.27'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.27"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.27'

BridgeDb 3.0.26

Minor release fixing the instantiation of Ensembl identifiers from their Bioregistry compact identifiers.

BridgeDb 3.1.1

Update release for the BridgeDb 3.1 series. It brings in the changes in the 3.0.24 and 3.0.25 releases.

Full Changelog: release_3.1.0...release_3.1.1

BridgeDb 3.0.25

Major release with important API change: the upgrade to RDF4J 4 required some BridgeDb Java APIs in the RDF modules to change from URI to IRI. Also updates to BridgeDb Datasources 20231202 and dependency updates for slf4j and JUnit.

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>3.0.25</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.25'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.25"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.25'

Full Changelog: release_3.0.24...release_3.0.25

BridgeDb 3.0.24

Minor release that updates the hardcoded links to the BridgeDb Webservice to use HTTPS. It also fixes a compile issue on some platforms and updated the Maven WAR plugin. Thanks to Tooba Abbassi Daloii and Alex Pico for patches!

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>3.0.24</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.24'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.24"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.24'

Full Changelog: release_3.0.23...release_3.0.24

BridgeDb 3.1.0

Minor change, big impact: this is the UniProtKB release, where the full name of the S data sources is changed. Any downstream use that depends on the full name to find the UniProt datasource may be affected. We introduced some backwards compatibility, but be aware of unexpected behavior.

Full Changelog: release_3.0.23...release_3.1.0

BridgeDb 3.0.23

Minor release that is mostly interesting for people using the Quality Control (QC) tool, where two bugs are fixed. Also updated Guava to version 32, fixes a small JavaDoc issue, and add a Java 8-based pom.xml specifically for PathVisio.

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>3.0.23</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.23'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.23"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.23'

Full Changelog: release_3.0.22...release_3.0.23

BridgeDb 3.0.22

Minor release that updates a few dependencies, adds the missing DataSource.bioregistryPrefixExists() method, adds PubMed Central and Mondo as data sources, and updates some debug/error to write BridgeDb with a lower case b.

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>3.0.22</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.22'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.22"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.22'

Full Changelog: release_3.0.21...release_3.0.22