BridgeDb release series

Egon Willighagen

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Nov 5, 2023, 8:37:06 AM11/5/23

to bridgedb-discuss

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

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Jul 30, 2024, 5:13:42 AM7/30/24

to bridgedb-discuss

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

--

Okay, you make FAIR. But why? We now can link FAIR maturity indicators to reuse case scenarios. You can top asking "Is my data FAIR?" and start asking "How FAIR do I need to be to allow that reuse?" Read about it in our new paper "FAIR assessment of nanosafety data reusability with community standards", https://www.nature.com/articles/s41597-024-03324-x

Egon Willighagen

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Jan 6, 2026, 3:20:57 AMJan 6

to bridgedb-discuss

Hi all,

time for another update. I have to cut down on the work done on the Java stack and can no longer justify maintaining three different versions of BridgeDb Java.

On Tue, 30 Jul 2024 at 11:13, Egon Willighagen <egon.wil...@gmail.com> wrote:

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.

I just released BridgeDb Java 3.0.30, and this will be the last one in this series. I have not yet released the "-java8" version of this release, but will do so soon. I will make a branch into series/3.0 and remove all BridgeDb modules not needed by PathVisio 3. I am not sure in which order I will do that. So, 3.0.30 is the last general purpose BridgeDb Java in this series.

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.

Here, I will sync with BridgeDb Java 3.0.30 and release 3.1.5 and 3.1.5-java8. This 'series/3.1.0' branch I will keep around a bit longer, until PathVisio 4.0 is officially out...

But...

I will move the BridgeDb Java 4.x branch to 'main' and that will be the default version for anything using BridgeDb Java other than PathVisio 3. That includes the BridgeDb Webservice, BridgeDbR, and at least Bacting. This will require Java 17 as a minimal version, much needed, because we are running a very old Apache Derby version, which adds to the time needed to maintain three versions.

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

--
Okay, you make FAIR. But why? We now can link FAIR maturity indicators to reuse case scenarios. You can top asking "Is my data FAIR?" and start asking "How FAIR do I need to be to allow that reuse?" Read about it in our new paper "FAIR assessment of nanosafety data reusability with community standards", https://www.nature.com/articles/s41597-024-03324-x

--

E.L. Willighagen
Department of Translational Genomics

NUTRIM Institute of Nutrition and Translational Research in Metabolism
Maastricht University
Blog: https://chem-bla-ics.linkedchemistry.info/

Chris Evelo

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Jan 6, 2026, 5:30:08 AMJan 6

to bridgedb-discuss

Hi Egon,

Nice to see so much progress.

I wondered about UniProtKB though. Although physiology is finally determined by proteins it is the genes that determine which ones are really available. And while in extreme cases one gene can code for multiple proteins, and in fact more often for multiple splice variants, the situation where multiple genes code for the same protein is at least as disturbing. I am not sure about the consequence. Making the genes central always intuitively felt more logical to me, but you could make an argument either way. In the end you want to be able to find all the gene products for a gene and all the genes coding for a protein.

Best wishes, and happy New Year to all of you, Chris

Egon Willighagen

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Jan 6, 2026, 5:47:32 AMJan 6

to bridgedb-discuss

Hi Chris,

happy new year!

What exactly are you wondering about UniProtKB? We are not using UniProt for gene/protein mappings, and it is not clear to me what consequence you are thinking about. Can you clarify?

Egon

Chris Evelo

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Jan 7, 2026, 3:41:33 AMJan 7

to bridgedb...@googlegroups.com

HI Egon,

Sorry, I reread your message. Somehow I thought you were suggesting to use Uniprot as the central database, but you indeed did not write that at all. I must have misread that the first time.

Best wishes, Chris

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