BridgeDb NWO grant update #6: second hackathon

This week the 2nd NWO Open Science BridgeDb grant hackathon took place. In all honestly, I had hoped we could open it up to a much larger community, but in our defense, the grant team is small, and we were flooded with various viruses in The Netherlands. Second, we need to get a lot if community feedback on additionally needed identifier mapping needs, except for support for Simple Standard for Sharing Ontological Mappings (SSSOM). This needs, however, more coding and we do not have the resources for that right now. Nevertheless, we had a great hackathon with people involved in the grant, including several people from other projects (aka "matching").

Projects

Before the meeting, several project ideas were written down, mostly related to remaining open tasks of the grant proposal (see Update #5). On the first day, the BridgeDb 3 Docker and BridgeDb Webservice JSON support were merged, which actually made sense. The work of Helena, Marvin, Ozan, and Javi paid off. The new docker is on DockerHub, automatically made with GitHub Actions (see top right screenshot). The overcame multiple small issues, like CORS support, port matching, dynamic configuration, etc. But this Docker should be easily deployable and allow projects like VHP4Safety and EOSC automagically keep up with the latest BridgeDb software and data.

Other projects focused on ID mapping databases. Myself, I worked on the first nanomaterial ID mapping database, an idea that was first pitch back in 2013 in the eNanoMapper proposal. So far, there was so little data and databases around, the ID mapping was never really needed. For this, updates were needed new releases in BridgeDb Datasources and BridgeDb Java. This is, fortunately, changing. Along the process Tooba and Ammar worked out a short recipe how to inspect the content of BridgeDb ID mapping databases, which technically are Apache Derby files.

At the end of the meeting, I updated the BridgeDbR package (2.9.1) with the latest Java libraries and looking into the technical possibility of a PathVisio3 release with the latest BridgeDb. But we really need a NWO Open Science or eScience Center grant for PathVisio to continue the work started by the COVID19 ZonMw grant. Funders that want to support important life sciences research are strongly encouraged to contact us and help us write the grant proposal that they want to fund.

Next

The grant funding is about the run out and its contribution to our research software position is too. As such, our focus is now going to be on the writing of the final reporting. This hackathon greatly contributed to the results and it was a wise decision to include those in the grant proposal.

Previous updates

• BridgeDb NWO grant update #5: BioHackathon, Webservice, Bioregistry
• BridgeDb NWO grant update #4: Bioregistry.io and a BioSB workshop
• BridgeDb NWO grant update #3: Pandora's box
• BridgeDb NWO grant update #2: building up momentum
• BridgeDb NWO grant update #1: first steps