SPARQL examples: SIB model, software, and patches

Jerven Bolleman et al. recently published a great preprint about how to use RDF to give SPARQL queries context by linking it (semantically) with metadata. The context includes keywords, the SPARQL endpoint the query can be run against, and a human-oriented description of the query. A few groups have at recent hackathons been working on usingn the combination of a SPARQL query and a human-oriented description to train large language models, including the group behind this paper. Given that SPARQL is a very small language, I can see this may work well, and that it may support our VHP4Safety and Scholia projects. 1 minute read

Mastodon, RSS, BlueSky

The x-odus continues and there is a wave of researchers moving from X to another walled-garden called Bluesky. This is good and bad. First, it is good that people are leaving X (imho) and it is good that they move to a platform that supports open standards, the AT Protocol. But I am less sure, about moving to another closed source platform. I prefer Mastodon. You can follow Mastodon accounts with their RSS feeds and that gives BlueSky users the ability to follow me on social media. This is important to me. I have a LinkedIn account too, but you can only follow me there if you have an account there too. To me, that does not align with the Open Science ideals. 1 minute read

Additional files, data, datasets, databases, and published data

Open Science doesn’t make publishing easier. That that’s all for the better: our research efforts are complex, so why should the publishing be. Sure, I am not talking about references formatting or moving the Methods section to the right location, or some silly statement that all authors agree with the manuscript when you are the only author. 6 minute read

New paper: The Virtual Human Platform for Safety Assessment (VHP4Safety)

I have not posted a lot about our Virtual Human Platform for Safety Assessment (VHP4Safety) project yet. Actually, more generally I do not post frequently about the funded projects. This is likely that few of them are Open Science by contract and often they have some formal process in place to approve output. That makes open notebook science-style posting about these projects hard. One is restricted to previously cleared material. 1 minute read

NASA Transform to Open Science (TOPS) Open Science 101

It was on my radar for some time already, but did not get around to finishing it. But I completed all five modules of the NASA Transform to Open Science (TOPS) Open Science 101 (doi:10.5281/zenodo.10161527). This Open Science 101 consists of several modules, starting with The Ethos of Open Science, via Open Tools and Resources, Open Data, and Open Code, to Open Results. 1 minute read

Patents, societal impact, and sustainability

Division 1 of our Institute of Nutrition and Translational Research in Metabolism (NUTRIM) held a meeting last week which had a panel discussion on the use of patents to bring research to the market, aimed at PhD candidates of the institute. Patents are one of the routes to make research output more sustainable. For example, the research output into a new method to study something or make something often needs the development into a product. For example, a new multivariate statistics method may need a graphical user interface. As such, the “development” after the research (think, R&D) is often part of the sustainability of some research. 4 minute read

Better Publishing

If you read my blog, it should not surprise you that I have long experimented with technologies to improve knowledge dissemination, for example in HTML. And I have blogged about publishing from an author and researcher, and editor perspective, for many years (see this longer list on my old blog). Also, in the Journal of Cheminformatics we pushed for innovation, including ORCID and GitHub adoption and Citation Typing Ontology adoption. 2 minute read