org.bridgedb.examples - BridgeDb 3.0.29

This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various dependencies.

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.28...release3.0.29

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.29</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.29' For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.29"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.29'

- Java
Published by egonw 7 months ago

org.bridgedb.examples - BridgeDb 3.1.4

Minor update to BridgeDb Java 3.1.3, fixing some Java 8 issues.

- Java
Published by egonw about 1 year ago

org.bridgedb.examples - BridgeDb 3.0.28

This update release brings in BridgeDb Datasources 20240925, a new organism (Rosmarinus officinalis), and various dependency updates, including an update of the MySQL driver.

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.27...release3.0.28

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.28</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.28' For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.28"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.28'

- Java
Published by egonw over 1 year ago

org.bridgedb.examples - BridgeDb 3.1.2 (Java 8)

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

- Java
Published by egonw over 1 year ago

org.bridgedb.examples - 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: https://github.com/bridgedb/BridgeDb/compare/release3.1.1...release3.1.2

- Java
Published by egonw over 1 year ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.27</version> </dependency> </dependencies>

For Gradle:

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

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

For Buildr:

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

- Java
Published by egonw over 1 year ago

org.bridgedb.examples - BridgeDb 3.0.26

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

- Java
Published by egonw over 1 year ago

org.bridgedb.examples - 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: https://github.com/bridgedb/BridgeDb/compare/release3.1.0...release3.1.1

- Java
Published by egonw about 2 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.25</version> </dependency> </dependencies>

For Gradle:

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

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.24...release3.0.25

- Java
Published by egonw about 2 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.24</version> </dependency> </dependencies>

For Gradle:

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

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.23...release3.0.24

- Java
Published by egonw over 2 years ago

org.bridgedb.examples - 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: https://github.com/bridgedb/BridgeDb/compare/release3.0.23...release3.1.0

- Java
Published by egonw over 2 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.23</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.22...release3.0.23

- Java
Published by egonw over 2 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.22</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.21...release3.0.22

- Java
Published by egonw almost 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.21</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.20...release3.0.21

- Java
Published by egonw almost 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.20</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.19...release3.0.20

- Java
Published by egonw about 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.19</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.18...release3.0.19

- Java
Published by egonw about 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.18</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.17...release3.0.18

- Java
Published by egonw about 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.17</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

Full Changelog: https://github.com/bridgedb/BridgeDb/compare/release3.0.16...release3.0.17

- Java
Published by egonw about 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.16</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw over 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.15</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw over 3 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.14</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw almost 4 years ago

org.bridgedb.examples - BridgeDb 3.0.13

Updated dependencies for log4j (2.17.1), OpenRDF (2.7.16), Apache CFX (3.2.14), and some dependency cleanup.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.13</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.13'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.13"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.13'

- Java
Published by egonw about 4 years ago

org.bridgedb.examples - BridgeDb 3.0.10

Updated dependencies. Everyone using BridgeDb in a (web)service context should upgrade as soon as possible.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.10</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.10'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.10"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.10'

- Java
Published by egonw about 4 years ago

org.bridgedb.examples - BridgeDb 3.0.9

This release is mostly identical to BridgeDb 3.0.8 but should have better OSGi support.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.9</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.9'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.9"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.9'

- Java
Published by egonw about 4 years ago

org.bridgedb.examples - BridgeDb 3.0.8

This release updates the URL patterns for the CAS database, adds Brassica napus as species, outputs info from Derby databases with the quality control (QC) tool, and adds Guide to Pharmacology Targets as 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.8</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.8'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.8"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.8'

- Java
Published by egonw over 4 years ago

org.bridgedb.examples - BridgeDb 3.0.7

This release updates a few dependencies, including jaxws-ri, log4j, and org.apache.cxf.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.7</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.7'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.7"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.7'

- Java
Published by egonw over 4 years ago

org.bridgedb.examples - BridgeDb 3.0.6

Another minor release doing a bit of code clean up and improves the output of the QC tool for readability.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.6</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.6'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.6"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.6'

- Java
Published by egonw over 4 years ago

org.bridgedb.examples - BridgeDb 3.0.5

Minor release that addresses a few data source inconsistencies and adds the DataSource.getCompactIdentifierPrefix() method.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.5</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.5'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.5"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.5'

- Java
Published by egonw almost 5 years ago

org.bridgedb.examples - BridgeDb 3.0.4

First public release of BridgeDb 3.0, a major version upgrade. It includes all the many small updates in the 2.3 seriese, but also introduces new features: support for secondary identifiers (identifiers that are not removed or deleted yet, but which have a better identifier), compact identifier support, no longer has the main copy of datasources.tsv, updates the versions of many dependencies, and a tool for create VoID header files. Java 8 and 11 are supported

This version has now seen several months of use in production and everyone is recommended to upgrade to BridgeDb 3.0.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>3.0.4</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.4'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.4"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:3.0.4'

- Java
Published by egonw almost 5 years ago

org.bridgedb.examples - BridgeDb 2.3.10

This larger minor release updates removes the Ant build system, and can now generate OSGi bundles with Maven (for five modules). It also gives more informative error messages when loading a Derby files goes bad, e.g. when BridgeDb 3 Derby files are attempted to be opened. Furthermore, it adds two Daphnia species and an Unspecified to the Organism enumeration.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>2.3.10</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.10'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.10"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:2.3.10'

- Java
Published by egonw over 5 years ago

org.bridgedb.examples - BridgeDb 2.3.9

This minor release updates the URL pattern for Scholia and bumps the versions of two dependencies, Apache Velocity and Google's Guava.

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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>2.3.9</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.9'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.9"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:2.3.9'

- Java
Published by egonw over 5 years ago

org.bridgedb.examples - BridgeDb 2.3.8

This minor release adds Guide to Pharmacology Targets 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>2.3.8</version> </dependency> </dependencies>

For Gradle:

gradle compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '2.3.8'

For Ivy:

xml <dependency org="org.bridgedb" name="org.bridgedb.bio" rev="2.3.8"/>

For Buildr:

buildr 'org.bridgedb:org.bridgedb.bio:jar:2.3.8'

- Java
Published by egonw almost 6 years ago

org.bridgedb.examples - 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:

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

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw almost 6 years ago

org.bridgedb.examples - 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:

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

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw almost 6 years ago

org.bridgedb.examples - 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:

xml <dependencies> <dependency> <groupId>org.bridgedb</groupId> <artifactId>org.bridgedb.bio</artifactId> <version>2.3.5</version> </dependency> </dependencies>

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by egonw almost 6 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw over 6 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw over 6 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw almost 7 years ago

org.bridgedb.examples - BridgeDb 2.3.1

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

- Java
Published by egonw about 7 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw almost 8 years ago

org.bridgedb.examples - 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

- Java
Published by egonw over 8 years ago

org.bridgedb.examples - 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:

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

For Gradle:

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

For Ivy:

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

For Buildr:

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

- Java
Published by stain over 8 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw over 8 years ago

org.bridgedb.examples - BridgeDb 2.1.3 Open PHACTS internal release

Internal BridgeDB release for Open PHACTS 2.1

Also available from myGrid's Maven repository

- Java
Published by stain almost 10 years ago

org.bridgedb.examples - 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/

- Java
Published by stain about 10 years ago

org.bridgedb.examples - 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.

- Java
Published by egonw about 10 years ago

org.bridgedb.examples - 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

- Java
Published by JonathanMELIUS over 10 years ago

org.bridgedb.examples - 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

- Java
Published by JonathanMELIUS over 11 years ago