This is my last post on blogger.com. At least, that is the plan. It has been a great 18 years. I like to thank the owners of blogger.com and Google later for providing this service. I am continuing the chem-bla-ics on a new domain: https://chem-bla-ics.linkedchemistry.info/ I, like so many others, struggle with choosing open infrastructure versus the freebie model. Of course, we know these things come and go. Google Reader, FriendFeed, Twitter/X (see doi:10.1038/d41586-023-02554-0). My new blog is still using the freebie model: I am hosting it on GitHub. But following the advice from a fe ..read more

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide's 'a CRC quick reference handbook' from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements. I just need a few SPARQL queries to list to which statements the qualifiers needs to be added. Basically, all boiling points which has the book as a ref ..read more

Just a quick note: I just love the level of detail Wikidata allows us to use. One of the marvels is the practices of 'named as', which can be used in statements for subject and objects. The notion and importance here is that things are referred to in different ways, and these properties allows us to link the interpretation with the source. For example, Max Born's seminal work Zur Quantenmechanik (doi:10.1007/BF01328531) uses a very short notation to cite other literature, as footnotes, and DOIs did not exist yet. So, in Wikidata, you can capture this like this ..read more

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a blog planet. Blog planets aggregate blogs from many people around a certain topic. It's like a forum, but open, free, community driven. It's exactly what the web should be. It turned out that planets do still exist, so I started a small corner on Wikidata: Q121134938, and a number of existing blog planets: The software used to run these planets is ancient, though. We need a new generation of software, replacing things like Planet. And I want somethin ..read more

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. So, time to migrate this blog :) This is probably a multiyear project, so feel free to continue reading it hear. Why? Because I start with the old posts :) Along the way, I am fixing things, improving it. I still have plenty on my todo list, but already ha ..read more

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. For example, Radboud University (>1k followers) already joined the Fediverse (Mastodon etc), making them independent from non-EU law and commercial interests. Scientific journals, Nobel Prize winners, etc already ..read more

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. Sadly, I am not aware of literature that compares the quality of peer review in databases with that in scientific journals. Also long overdue, in my opinion ..read more

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. Since then, I reviewed two more papers. One of these latter two was not a more traditional paper, but a different kind of research output: a definition, about "Drive-by Curat ..read more

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. You can even follow WikiPathways's account with its RSS feed. Dissemination should not be paywalled. Maybe Musk has been talking to Elsevier and Sprin ..read more

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. This series of posts is a number of things toxicology projects can do to benefit from ELIXIR solutions ("services"). The posts have been sent first to the ELIXIR Toxicology Community mailing list (please join!). History In this post, let's look at FAIRsharing. It is "A curated, informative and educational resource on data and metadata standards, inter-related ..read more