New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that making something usefully findable requires deep indexing, and already that continues to be difficult, because we are not seeing it enough. So, when I thought convert a paper led by Hoet’s lab in Leuven into machine-actionable RDF to make it FAIR, I gravely underestimated the amount of work. Jeaphianne et al. did an awesome job on this work (doi:10.1186/s13321-024-00833-0). 1 minute read

cdk2024 #2: publishing grant proposals

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit. less than 1 minute read

cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit

We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant. 1 minute read

Open Science Retreat #2: CiTO Nanopublications

During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on the topic. The nanopub.net website describes that [a nanopublication is a small knowledge graph snippet with metadata that is treated as an independent (scientific) publication.]. The knowledge graph, it continues, can be anything from an opinion to the link between a disease and a gene (doi:10.1109/ESCIENCE.2018.00024). 4 minute read

Open Science Retreat #1: impressions

Last week I attended the Open Science Retreat (#osr24nl) in a quite and relaxing region in North-Holland. The meeting was how I like all meetings to be (and I count myself lucky many of my meetings are like this): open, welcoming, constructive, diverse, and intellectually challenging. Not all scientific meetings are like this and it is easy to end up going to obligatory meetings where the discussions are of a different level. Therefore, great thanks to the organizers, but also to all participants, that showed not just to have a hearth for open science (getting pretty common), but also a drive to advocate for open science. Finally, I like to thank the people that joined me in creating nanopublications for CiTO annotations (will blog about that later), and to Sadik and Marija with whom we worked on exploring using Wikibase for capturing knowledge about research waste in ecology (more about that later too). less than 1 minute read

Reusing data: two new papers

My research is about the interaction of (machine) representation and the impact on the success of data analysis (matchine learning, chemometrics, AI, etc). See the posts about molecular chemometrics. This got me into FAIR: making data interoperable and being able to (really) reuse data is the starting point of doing research. 1 minute read

New paper: "Wikidata subsetting: approaches, tools, and evaluation"

Just before the end of the year, the Wikidata subsetting: approaches, tools, and evaluation paper by Seyed Amir Hosseini Beghaeiraveri et al. got published (doi:10.3233/SW-233491). I am really excited our group (i.e. Ammar and Denise) has been able to contribute to this. I think it also is a great example of the power of hackathons to bring together people. 1 minute read