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: Actually, you see one pull request here that I closed. I accidentally included a circular dependency.

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. I opened the session with a few slides welcoming everyone at Maastricht University (and our Dept of Translational Genomics, and explaining the NWO grant.

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.

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 A database should not contain knowledge based on (only) a retracted article.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: The idea is far from new and has been around for two decades. But the two Beilstein journals (both diamond Open Access), actually integrated into their active publishing model. That has been trialed and put in action before.

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.

With a year of preparation and two years of thinking, on September 1st 2024 the Department of Bioinformatics, aka BiGCaT, merged with two other departments to form the Department of Translational Genomics (see also this LinkedIn announcement). This merger creates many new opportunities while it strenghtens our bioinformatics research.

I wish I could say I remember the first citation to one of my research articles. I do not. But I do remember the excitement to see why someone was citing my research. What I do remember is that I got a comment around the same time along the lines of this: “why would anyone cite your article if they can download the results for free?” (about open science cheminformatics research). Other times.

One-and-a-half years ago I started migration my blog from blogger.com to a Markdown and Git-based blog. It has been a fascinating journey that I do not regret.