A lot is happening. If you have been following this project more closesly, you may have already seen some interesting updates, but I will post it here too. First, a quick recap. In March I started a new Blue Obelisk project to collect CCZero IUPAC names from primary literature (paper still pending). It turned out we can automate that, while legally not violating any laws or licenses.
Mike Taylor wrote up a post about the various things a journal article is doing, the first being a scientific report . We put a lot of money in establishing a scientific track record. In the past 30 years how we publish our research and how we archive it has changed significantly. If you read my blog more often, you know I have been critical of the performance of many publishers.
A recent report by the Dutch RIVM, PFAS in the blood of the Dutch population (doi:10.21945/RIVM-2025-0094), writes that seven PFAS compounds are found in blood samples of all tested people. Another nine compounds are found in at least 1-in-10 people. Because there is relevant data in the report on the 28 studied PFAS compound, I wanted to have the report more FAIR than it is on the website. Why this report?
Depending on your exact definition of doing science, keeping track as precise as possible of your observations is an essential part of doing science. The precision should be high enough that mistakes are obvious. This pattern is, of course, not limited to doing science and we see this in open source development too. Unfortunately, in the modern way of doing science, this is not getting the attention it should get.
One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed for new papers of a biohackathon.
I could not find the time earlier to report (reason), but three weeks ago we passed the fourth milestone release of the CCZero IUPAC names found in literature collection. This release contains 200026 IUPAC names, 168702 unique names, reflecting 116207 unique InChIKeys. Time for an update of the One Million IUPAC names project.
Last week, the Wikidata and Sister Projects event tooks place. The presentations are recorded, and I strongly encourage you to check the schedule.
This week the 13th International Conference on Chemical Structures took place (see also this Scholia overview or this overview of the full ICCS history). This is the conference I first joined 20 years ago as a PhD student presenting a poster (see these past blog posts). Of course, I am actually co-organizer nowadays (actually, co-treasurer). Organizing a meeting with just over 200 participants, and I like to thank Gerard and Willem in
Two week ago I uploaded a paper that has been in the works for some time. In fact, I first mention it as conference paper for the special issue of the 11th International Conference on Chemical Structures, you know, the meeting held in 2018, of which the 13th edition starts in 7 days. I had a poster at that conference which I described in this blog post.
INTOXICOM is an ELIXIR Toxicoloy Community (doi:10.12688/f1000research.74502.2) implementation study, organizing five workshops, each one with a different topic. The first three workshops were in Utrecht (doi:10.37044/osf.io/un2rw), Basel, and Uppsala.
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 milestone release took a bit longer. Going from 50 to 100 thousand is a bigger step than from 10 to 50 thousand, but the open access chemistry literature was already done by then. Basically, I ran out of open access chemistry publications.