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

Rescuing Scholia #2: getting closer

Three weeks ago, I wrote a the post Rescuing Scholia: will we make it in time?, where I sketched a future without Scholia. Scholia, started almost 10 years ago and I think it is worth keeping around longer. 2 minute read

Open Infrastructures #1: Research Software Directory

Research software is an integral part of scientific investigations. 1 minute read

Rescuing Scholia: will we make it in time?

What started out in 2016 on Twitter became a (small) award winning decade long collaborative project. Unfortunately, the future is not clear. We are at odds if it will survice the growth of Wikidata and in particularly the SPARQL graph split. To be clear, the choice for Blazegraph initially worked great, but after it was bought by a big company, developed halted. Very unfortunate for Wikidata. Unlike earlier, we no longer have funding, and rewriting Scholia at this scale takes a good bit of effort. We already held a few hackathons. 1 minute read

WikiPathways curation reports on profile pages

I have been running automated curation tests for many years now, at least from before 2018. Because it has been done without funding, it has not been as nicely integrated, and depends, for example, first on the RDF generation to be integrated in the GitHub Action. So, I still run them regularly (often in the morning during breakfast). Meanwhile, the curation tests help the project to monitor and maintain the quality of the pathways. The curation reports have been integrated into pathway pages for some time now. less than 1 minute read

20 years of blogging

Today, exactly 20 years ago I started this blog. Two years ago I decided to upgrade my blog to one with version control. A decision I am still very excited about. It allowed me to start innovating my blog again. As part of this, and following the step Lars took ealier, I registered my blog with Rogue Scholar and I started migrating blog posts from blogger.com to my new location. I completed the years 2005, 2006, 2007, and 2008 now. 1 minute read