Last year, Denise, Tina, Marvin, and I received an NWO Open Science grant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel (see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work part-time on this grant.

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong.

Publishing habits changes very slowly, too slowly. The whole industry is incredibly inert, which can lead to severe frustration as it did for me. But sometimes small changes can do so much.

Rough timeline of the Journal of Cheminformatics. The linked PDF has linked years with references. In this open letter, I will explain why I intend to step down as Editor-in-Chief of the Journal of Cheminformatics, which also happens to be a Springer Nature journal.

The BridgeDb project (doi:10.1186/1471-2105-11-5) (and ELIXIR recommended interoperability resource) has several aims, all around identifier mapping:

Last week the third paper got published in the Citation Typing Ontology Collection and this weekend I finished adding the citation annotations to Wikidata.

During the time of the editorial about the Journal of Cheminformatics Citation Typing Ontology (CiTO) Pilot I already worked out a model to add CiTO annotation in Wikidata.

WP4846 that I started on March 16. It will see a massive overhaul in the next weeks. Voices are getting stronger over how important Open Science is. Insiders have known the advantages for decades. We also know the issues in the transition, but the transition has been steady.

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another.

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another.

A figure from the article, outlining the idea of using SPARQL queries to extract data from the open knowledge base. As a reader of my blog, you know I have been doing quite some research where Wikidata has some role. I am preparing a paper on the work I have done around chemicals in Wikidata, based on what I presented at the ICCS with a poster.