BridgeDb release series

[Egon Willighagen]

Hi all,

some news from my side. The NWO Open Science grant is over now, for some months already, but most of the work is completed and we have a well-functioning updated BridgeDb Webservice [0]. New features include JSON support, built-in OpenAPI interface, and a greatly reduced size (<9MB, excluding data).

On the BridgeDb Java side a lot is happening too. During the NWO grant we factored out the webservice, and factoring out other extensions of the code library is planned. We will also undergo a transition in a key datasource, UniProtKB, and migrate to require at least Java 11.

To accommodate this, we will have a transition phase with various BridgeDb Java series (for as long as needed):

- BridgeDb Java 3.0.x: currently 3.0.23, and this will only see bug and security fixes

- BridgeDb Java 3.1.x: the UniProtKB update (3.1.0 was release today [1])

- BridgeDb Java 4.x: to be started soon requiring Java 11 and which will factor out extension

With kind regards,

Egon

0.https://github.com/bridgedb/BridgeDbWebservice/releases

1.https://github.com/bridgedb/BridgeDb/releases/tag/release_3.1.0

--

"Artificial intelligence for natural product drug discovery". Do I need to say more? https://doi.org/10.1038/s41573-023-00774-7

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://social.edu.nl/@egonw
PubList: https://orcid.org/0000-0001-7542-0286

[Egon Willighagen]

Hi all,

a quick update.

BridgeDb Java 3.0.x: I just released 3.0.27. Please check the recent releases. This version supports Java8 for the core (see the pom-java8) and has the old UniProt datasource.

BridgeDb Java 3.1.x: I am about to release 3.1.2. This is basically the same as the 3.0.x series (in fact, synched with 3.0.27), BUT uses the new "UniProtKB" datasource name.

I will also update the BridgeDb Webservice soon, updating this to 3.0.27.

Egon

On Sun, 5 Nov 2023 at 14:35, Egon Willighagen <egon.wil...@gmail.com> wrote:

On the BridgeDb Java side a lot is happening too. During the NWO grant we factored out the webservice, and factoring out other extensions of the code library is planned. We will also undergo a transition in a key datasource, UniProtKB, and migrate to require at least Java 11.

To accommodate this, we will have a transition phase with various BridgeDb Java series (for as long as needed):

- BridgeDb Java 3.0.x: currently 3.0.23, and this will only see bug and security fixes

- BridgeDb Java 3.1.x: the UniProtKB update (3.1.0 was release today [1])

- BridgeDb Java 4.x: to be started soon requiring Java 11 and which will factor out extension

With kind regards,

Egon

0.https://github.com/bridgedb/BridgeDbWebservice/releases

1.https://github.com/bridgedb/BridgeDb/releases/tag/release_3.1.0

--

"Artificial intelligence for natural product drug discovery". Do I need to say more? https://doi.org/10.1038/s41573-023-00774-7

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://social.edu.nl/@egonw
PubList: https://orcid.org/0000-0001-7542-0286

--

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