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

BridgeDb 3.0.21

Minor release that a few NullPointerExceptions in the QC tool, migrated the VoID tool into a separate org.bridgedb.tools.voidtool module, add Prymnesium parvum and Skeletonema marinoi as new species, and removes to plugin for the discontinued Taverna.

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>3.0.21</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.21'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.21"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.21'

Full Changelog: release_3.0.20...release_3.0.21

BridgeDb 3.0.20

Minor release that fixes a typo in the VoID tool, adds OSGI support for the org.bridgedb.webservice.bridgerest module, and ensures the version.props is shipped with the jars.

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>3.0.20</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.20'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.20"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.20'

Full Changelog: release_3.0.19...release_3.0.20

BridgeDb 3.0.19

Minor release that updates to BridgeDb DataSources 20230208, bringing in three nanomaterial data 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>3.0.19</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.19'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.19"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.19'

Full Changelog: release_3.0.18...release_3.0.19

BridgeDb 3.0.18

Minor release that updates the versions of several dependencies, including Apache Derby 10.15.2.0, handling ChEBI identifiers with Bioregistry better, and a much cleaner BridgeDb QC tool.

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>3.0.18</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.18'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.18"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.18'

Full Changelog: release_3.0.17...release_3.0.18

BridgeDb 3.0.17

Minor release that adds categories for data sources, allowing tools to filter based on category. It adds Caulobacter vibrioides as species, and contains a good number of JavaDoc 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>3.0.17</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.17'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.17"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.17'

Full Changelog: release_3.0.16...release_3.0.17

BridgeDb 3.0.16

Minor release with some further clean up and one new functionality during the first NWO Open Science grant hackathon. Data sources no longer have just a main type but also categorical tags, which can be used to filter them more easily.

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>3.0.16</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.16'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.16"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.16'

BridgeDb 3.0.15

Second BridgeDb Java release funded by the NWO Open Grant (203.001.121). It adds Bioregistry.io support in the DataSource and Xref APIs. It also updates the OpenRDF dependency to RDF4J. This release adds some more testing and fixes a few minor inconsistencies. Finally, it adds a DataSource.mock() method similar to the register() method, but without the registration and just returning a mock DataSource.

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>3.0.15</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.15'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.15"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.15'

BridgeDb 3.0.14

First BridgeDb Java release funded by the NWO Open Grant (203.001.121), aimed at making the build process more robust (and adding a new developer). It updates a number of dependencies (Apache Velocity, Apache Derby, JUnit, Log4j, and MySQL driver) and add the first bits of Bioregistry.io support. This release also removes the BridgeDb Webservice, which is now available from a separate GitHub repository. The Xref.toString() now returns whether the identifier is primary or not, which is now also retrieved from the Derby database. It also update to the BridgeDb Datasources 20220526 release, which includes the Bioregistry prefixes for all data 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>3.0.14</version>
    </dependency>
</dependencies>

For Gradle:

compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.14'

For Ivy:

<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.14"/>

For Buildr:

'org.bridgedb:org.bridgedb.bio:jar:3.0.14'