BridgeDb NWO grant update #2: building up momentum

UML diagram showing the steps
in a BridgeDb webservice call.

Last month I reported on the start of the NWO Open Science grant and it is time for an update. First, our grant now has a grant number, 203.001.121. For a project that is about identifiers, having a project identifier is a big deal.

Some updates by Denise, Martina, Tooba, Helena, and me:

• the project proposal was accepted and published in RIO Journal (doi:10.3897/rio.8.e83031)
• we started drawing various BridgeDb stories as UML diagrams using Mermaid
• updated the documentation in the BridgeDb Webservice repository
• an Ensembl 104-based gene/protein ID mapping database (doi:10.5281/zenodo.6367091)
• better unit test coverage of the BridgeDb Java library
• various CITATION.cff updates

There are some further things cooking, including an updated datasources.tsv and a few pull requests. I expect a new release of the BridgeDb Java library before the end of the month.

With these new results, we also updated the ISAAC database for the two new products (the published proposal and the gene/protein ID mapping database):

Right now, the ISAAC database does not make it easy to add content. Instead, there is a series of forms that have to be manually filled, including separate forms for authors. You cannot simply add a DOI. Well, until recent. Lars Willighagen and I developed a Chrome browser add-on to help out (also works with Brave), using his awesome citation-js (doi:10.7717/peerj-cs.214). The above two entries in the database have been added using this add-on.

We hope it will help other NWO grant holders too and that the add-on becomes obsolete in the near future Because the ISAAC database needs some updates elsewhere too. For example, it does not seem to value open source and open data so much yet:

That is a shame.