cdk2024 #6: wrapping up already

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. We held a user group meeting earlier this month (btw, check out the slides by Jonas), and I have did a few more JUnit testing updates last week: 2 minute read

New preprint: "BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports"

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. Well, it was a big more complicated, but all the nicer to now have the project report online (doi:10.37044/osf.io/p9u42_v1). And once the ORCID was working, adding the Research Organisation Registry ID was not much harder. Cool to see both used in other recent BioHackrXiv reports! less than 1 minute read

cdk2024 #5: Chemistry Development Kit User Group Meeting - Day 2

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. The coding was not mostly only the CDK repository itself, but some things happened there too: 1 minute read

cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1

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. 1 minute read

One Million IUPAC names

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. 7 minute read

Retracted articles in Wikidata

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 A database should not contain knowledge based on (only) a retracted article.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. Similarly, it turns out that I am citing retracted articles in two papers (and a preprint of one of them). less than 1 minute read

Beilstein journals contain Bioschemas

Two weeks ago, the Beilstein Institute announced Bioschemas support in their journals: 3 minute read