BridgeDb NWO grant update #5: BioHackathon, Webservice, Bioregistry

Our new Mastodon account.

So, I had a lot of teaching and that besides project deliverables and final reports, a few project meetings, it left me with little time to blog my monthly BridgeDb NWO grant update. But here goes, as a lot did happen in the background.

First, some outreach:

• 2022-09-15, Open Science in Practice Webinar Series: BridgeDb and Wikidata: a powerful combination generating interoperable open research (video)
• 2022-10-20, UM Data Science Research Seminar: Making research output FAIR with Wikidata

Work Package 1

In WP1 we continued working on the core BridgeDb library (after we split out the BridgeDb Webservice into a separate repository). Last time we reported about Bioregistry support (used on the new WikiPathways website). I am happy this paper now got published. BridgeDb Java 3.0.16, 3.0.17, and 3.0.18 have been released. No big changes, but mostly additional features for WikiPathways and the upcoming libGPML and PathVisio 4.0. The latest release also comes with an updated BridgeDb Datasources.

Work Package 2

This is where the most work happened in the last few months. Helena has been working on the BridgeDb Webservice code. This code was 10 years old and desperately needed an upgrade. In the proposal we mention JSON, compact identifiers (or the CURIEs from Bioregistry), and more FAIRness. After a few weeks of learning the used REST library and hacking, Helena got content negotiation working and we are happy to report that the upcoming release will support JSON. Even better, it also solves the problem we had with the Docker image.

Work Package 3

Mapping databases continue to be updated. For the metabolite identifier mapping database, Denise has been looking into wrapping this in a Docker image and all future mapping databases will use schema 4 of the BridgeDb database schema (support primary/secondary identifier annotation). Denise, Martina, Tooba, and I participated in the ELIXIR BioHackathon Europe where we worked on several projects. Project 26 looked into more identifier mapping with Wikidata and PubChem and improving interoperability of the Bioschemas MolecularEntity profile. We also spoke with the TogoID team from Japan on interoperability and possibilities of collaboration.

Next

With a few months left until the end of the project, we are going to focus on wrapping up the progress. The webservice needs an updated OpenAPI documentation and a proper release and documentation how anyone can run a local BridgeDb Webservice easily (and we can update the EOSC instance). We also have a (ELIXIR) stakeholder-oriented workshop to organize.

Oh, and we created a Mastodon account: @bridgedb@fosstodon.org!

Previous updates

• 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