CiTO updates: Wakefield and WikiPathways

This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an update on my Citation Typing Ontology use cases. And I have to say, a mention by Silvio Peroni is pretty awesome, thanks! 2 minute read

New paper: "Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool"

I am still catching up with a lot of work, and found out I actually had forgotten to blog about this cool article by Denise Slenter: “Discovering life’s directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool” (doi:10.1039/D3DD00069A). This paper explains how various open science resources (Wikidata, Reactome, WikiPathways) are used to visualize the biological story of the data from two metabolomics experiments archived in MetaboLights. 1 minute read

GoatCounter, Rogue Scholar and more new things

About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago. 1 minute read

cdk2024 #3: an unexpected downstream project

In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The Groovy Cheminformatics with the Chemistry Development Kit book is a project that has run since 2009. 2 minute read

Two meetings: ELIXIR Toxicology and FAIR4ChemNL

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore. 1 minute read

New paper: FAIR assessment of nanosafety data reusability with community standards

Ammar is finishing up his PhD thesis with his research on the use of FAIR towards predictive toxicology. Or, “AI ready”, as the term FAIR is now sometimes explained. Any computational method needs good data, and just FAIR is not enough. It needs to meet community standards, as formalized in R1.3. To me, this includes meeting community standards like minimal reporting standards. Indeed, in the EU NanoSafety Cluster the notion that FAIR data also needs be scientifically good data is well noted. 1 minute read

New paper: A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials

I was about to call this blog post From spreadsheets to RDF, after the post last week. But then I decided to just use the pattern I typically use. Why I wanted to use that shorter term in the first place was that one of the thing I like about the AMBIT software (of OpenTox and eNanoMapper fame) is its RDF support (see doi:10.1186/1756-0500-4-487). But RDF, ontologies, those are hard things. And unlike mathematics, we do not have simple objects like integer numbers or simple operators. Well, I think we do, and we talk about them. But there is no obligatory education. Just like any biologist needs to know what 1 + 2 means, I think any biologist needs basic knowledge about how knowledge graphs work. But sometimes feels like a taboo, like cursing in the life sciences church. 1 minute read