Two and a half month into the One Million IUPAC Names project, we passed the third milestone, the one for 100 thousand IUPAC names (doi:10.5281/zenodo.15266459). Time for an update.
This is the third weekend I am working on Scholia, the first two part of the April 2025 hackathon. It follows the hackathons last year October and November hackathons. There is some urgency for this unpaid work, because Wikidata is splitting the RDF into two SPARQL endpoints (see this The Signpost and this post by Finn). This split has happened, but there is a legacy server for tools that have not been upgraded.
One reason to move my blog from Blogger to a git-backed repository is that I can update links but that the version history shows exactly what change was made.
Tomorrow is already the last day of the NWO Open Science grant for the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more to finish up the reporting.
While this was not the primary hack project during the ELIXIR BioHackathon Europe last autumn, but I really like BioHackrXiv and I got the question if I could have a look at getting the ORCID logo in generated PDF. The ORCID was already in the YAML metadata of report markdown, so it sounded easy.
Where the first workshop day had several talks about new and old features of the Chemistry Development Kit (CDK), the second day was a hackathon day. We hacked and we talked.
As part of our Dutch Research Council (NWO) Open Science grant, we organized a Chemistry Development Kit User Group Meeting (#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon.
Names of chemicals are part of the human user experience when browsing a chemical database. And literature too, of course. Chemical names are also not easy to use, and what a chemical name means is not always clear. This is why the IUPAC started a standardizing nomenclature in chemistry, the IUPAC names. Each IUPAC name uniquely defines the chemical structure it defines. For example, methane is the IUPAC name for the chemical CH4.
A good number of years ago, a colleague and I explored if we could get access to the Retraction Watch Database, but we could not afford it. We have been using data on retractions for curate our databases, like WikiPathways. A database should not contain knowledge based on (only) a retracted article. Wikidata, btw, has a small number (499) of statements supported by retracted articles.
Two weeks ago, the Beilstein Institute announced Bioschemas support in their journals:
This is mostly a test, but if it turns out the way I hope it will, likely after a few iterations, it adds support in my blog for CiTO intent annotations to the DOIs I cite. I pondered about the earlier.