I am a bit behind with tweeting about new published papers, but let that not reflect that these papers are not very exciting. The first paper is by Marvin an almost-finished PhD candidate in our group and now working as postdoc on the VHP4Safety project. He has been working on linking adverse outcome pathways (AOPs) with molecular pathways, such as in WikiPathways.

Part of the scientific program of the ICCS 2022.

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.

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.

The number of revisions and contributors for all pathways in the human pathway analysis collection.

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.