This blog is almost 18 years old now. I have long wanted to migrate it to a version control system and at the same time have more control over things. Markdown would be awesome. In the past year, I learned a lot about the power of Jekyll and needed to get more experienced with it to use it for more databases, like we now do for WikiPathways.

The role of a university is manifold. Being a place where people can find knowledge and the track record how that knowledge was reached is often seen as part of that. Over the past decades universities outsources this role, for example to publishers. This is seeing a lot of discussion and I am happy to see that the Dutch Universities are taking back control fast now.

I am pleased to learn that the Dutch Universities start looking at rankings of a more scientific way. It is long overdue that we take scientific peer review of the indicators used in those rankings seriously, instead of hiding beyond fud around the decline of quality of research. So, what defines the quality of a journal? Or better, of any scholarly dissemination channel? After all, some databases do better peer review than some journals.

A bit over a year ago I got introduced to Qeios when I was asked to review an article by Michie, West, and Hasting: “Creating ontological definitions for use in science” (doi:10.32388/YGIF9B.2). I wrote up my thoughts after reading the paper, and the review was posted openly online and got a DOI. Not the first platform to do this (think F1000), but it is always nice to see some publishers taking publishing seriously.

And just like that, without a warning, Twitter changed policies again, and you now need a Twitter account and be logged in to see public tweets: Twitter has started blocking unregistered users (The Verge). Though I learned it first via Mastodon, of course. For example, this is what happens when you go to twitter.com/wikipathways: Fortunately, WikiPathways does have a Mastodon account, that anyone can see without having a Mastodon account.

Some years ago we started the ELIXIR Toxicology Community. It has been an interesting journey, partly covered in this whitepaper). We started with interaction we had in several projects already, but particularly the potential. I see this.

When last week in a large (and relevant) Dutch research event ChatGPT came up, and that this was going to change the world. Even the critiques came up, but were effectively disregarded with “these methods get better very quickly”. This is not untrue, but not really true either. I murmur “not even wrong”. I know how hard it is to get computers to find meaningful patters; I did a PhD in this in the early 21st century.

I think that if you want to make your knowledge FAIR, you should use an open license and RDF. Simple. Now, not everything is knowledge. A lot of data is, but a lot more is not, think raw data. Using RDF to explain a protein sequence is still something that makes me feel uneasy. However, first, you need to make RDF, you need to make assumptions explicit, you need to decide on meaning. Making RDF is not easy.

Okay, the Pilot is over ending with 17 papers, 16 of which have CiTO annotations (and so far 4 J.Cheminform. papers after the pilot), but my interest in the Citation Typing Ontology continues and we just need more adoption. Datasets as source of annotations So, here’s a quick Wikidata update.

There are multiple initiatives to support the migration from Twitter to Mastodon (see also this blog post ). But Wikidata should not be forgotten here which has been tracking Mastodon accounts of things in their database: So, here are some Wikidata SPARQL queries to see the uptake: Universities with Mastodon All Mastodon accounts in Wikidata (or subset with also a Twitter account) Nobel Prize winners with Mastodon Academic

In August I reported about 2D depiction of (CX)SMILES in Wikidata via linkouts (going back to 2017). Based on a script by Magnus Manske, I wrote a Wikidata gadget that uses the same CDK Depict (VHP4Safety mirror) to depict the 2D structure in Wikidata itself: Note the depiction of the undefined (CIP) stereochemistry on two atoms. Thanks to Adriano and John for working that out.