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

PhD Defences: Andra Waagmeester and Marvin Martens

2023 has been a long year in which a lot happens. Two EU projects ended (RiskGONE and NanoSolveIT; more about that in a later post), our group leader Chris Evelo will retire this year, the ELIXIR Toxicology Community started (see this post), the new WikiPathways website launched (see this post), and a lot, lot more. 1 minute read

New paper: "WikiPathways 2024: next generation pathway database"

This week the next WikiPathways NAR Database issue paper was published (doi:10.1093/nar/gkad960). It is the next paper in a series of papers about the evolution of the Open Science project for making biological pathways available in a Open and FAIR way. This year, it described that significant move away from MediaWiki. It simply was too costly to keep up with the upstream code base (think: more than 200 thousand euro costly). This paper describes a transition to a modular system with Jekyll and Markdown as new platform technologies. The full details are available as open notebook science: everything is basically a git repository. less than 1 minute read

Artificial intelligence for natural product drug discovery

Two weeks ago the write up of a week-long scientific discussions around artificial intelligence for natural product drug discovery in Leiden at the Lorentz Center got published (doi:10.1038/s41573-023-00774-7, free PDF). less than 1 minute read

Using FAIR to select data for reuse

This paper got published in July already, but I had not had the time yet to blog about this exciting work by Irini Furxhi and Ammar Ammar: A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability (doi:10.1016/j.impact.2023.100475) 2 minute read

Making BridgeDb Derby files with Groovy

I just want to drop this here. There are various ways to make BridgeDb identifier mapping files. Some of the tools predate my joining the BiGCaT research group and the BridgeDb project, but this Groovy page is basically what we have been using to create the metabolite identifier mapping databases: 1 minute read