Rescuing Scholia #3: We did it!

It was not a set up, when I openly wondered if we would be able to rescue Scholia in time. I honestly did not know. Three weeks and some serious hacking by an international team later I was more optimistic. Actually, just before christmas, we started writing a SWAT4HCLS 2026 demonstration abstract. This was accepted and you can read the Scholia 2026: Compliance with SPARQL 1.1 preprint here and here. This paper describes the work that had to be done, and I am deeply grateful to everyone who contributed with smaller or bigger contributions (Daniel, Peter, Konrad, Johannes, Lars, Wolfgang, Hannah). I am merely first author for the demo, and just another contributor to the long series of patches, in a branch started by Prof. Hannah Bast. 1 minute read

Where do the WikiPathways come from?

WikiPathways was founded in 2008, in the year I left Wageningen (and we Nijmegen) and moved to Uppsala, Sweden. When we dediced to move back to The Netherlands in 2012, I got to opportunity to join the Department of Bioinformatics (BiGCaT) and work on Open PHACTS. I had visited the group in March 2011 because I had a COST action workshop near Maastricht (about nanoQSAR) and the bioinformatics group did WikiPathways. 5 minute read

The TDCC NES Col-Lab Retreat

Last autumn two TDCC projects started, FAIR4ChemNL (with the PeerTube channel and doi:10.61686/XVYQV45374) and FAIRify for metabolomics data (doi:10.61686/CSGIP04334). But I haven’t written much on either yet and what the role is our research group in these projects. 3 minute read

Open Infrastructures #2: the SURF Fediverse

When I first started writing this post, I started writing up why scientific communication is important, but because I started explaining what needs improving, and what are underlying causes why change is not happening, it got dark pretty quickly. So, I deleted that essay again. Instead, let’s just enjoy the awesome and long list of solutions we have for scientific discourse. Readers of my blog can find many posts in the past 20 years about the diversification. One thing I will say before I move one, is a reply to the argument that journal-based peer review is essential to the quality of research: if the quality of your research is dependent on your peers, then please rethink why you are doing research. 2 minute read

Chemical blogs history

Like many awesome internet phenomena, blogging started in the late nineties. Nature authors and editors recognized the effort early. In 2006 there were already more than 45 million blogs, and at least 50 science blogs made it in the top 50,000 and 5 in the top 3,500. 1 minute read

Where does the WikiPathways Cited In information come from?

I have been wanting to blog about this since this summer, but with everything going on, I never really got around to it. What is this Cited In feature of WikiPathways and where does that information come from? If you have not noticed this yet, this is what it looks like for WP4846: 6 minute read

PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge

Back on October I presented Everything you always wanted to know: plant pathway modelling in WikiPathways (doi:10.5281/zenodo.18149988) at the Knowledge Graphs for Plant and Microbiome Multiomics symposium (see this archived LinkedIn post) on 14th October 2025 (youtube recording). I had not found time yet to post about this meeting, but it was an awesome list of speakers, regrettable absense of some others, but resulting in new contacts and some slowly evolving collaborations. 2 minute read