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Monday, December 17, 2018

From the "Annalen der Pharmacie" to the "European Journal of Organic Chemistry"

2D structure of caffeine, also
known as theine.
One of my hobbies is the history of chemistry. It has a practical use to my current research, as a lot of knowledge about human metabolites is actually quite ancient. One thing I have trouble understanding that in a time where Facebook knows you better than your spouse, we have trouble finding relevant literature without expensive, expert databases, not generally available.

Hell, even the article that established that some metabolite is actually a human metabolite is not found within reasonable time (less than a minute).

This is one of the reasons I started working on Scholia, and the chemistry corner of it specifically. See this ICCS conference poster. The poster outlines some of the reasons why I like it, but one is this link between chemical structures and literature, here for caffeine:


You can see the problem with our chemical knowledge here (in Wikidata): before 1950 it's pretty blank. Hence my question on Twitter what journal to look at. A few suggestions came back, and I decided to focus on the journal that is now called the European Journal of Organic Chemistry but that started in 1832 as the Annalen der Pharmacie. I remember the EurJOC being launched by the KNCV and many other European chemistry societies.

BTW, note here that all these chemistry societies decided it was better to team up with a commercial publisher than to continue publishing it themselves. #Plan_S

Anyway, the full history is not complete, but the route from Annalen to EurJOC now is (each journal name has a different color):


That took me an hour or two, because CrossRef has for all articles the EurJOC journal name. Technically perhaps correct, but metadata-wise the above is much better. Thanks to whomever actually created Wikidata items for each journal and linking them by follows and followed by.

In doing so, you quickly run into many more metadata issues. The best one I found was a paper by Crasts and Friedel, known for the Friedel-Crafts reaction :) Other gems are researcher names like Erlenmeyer-Heidelberg and Demselben and Von Demselben.

Back to caffeine, an active chemical in coffee, a chemical many of us must have in the morning, is actually the same as theine. Tea drinkers also get their dose of caffeine. We all know that. What I did not know, but discovered while doing this work, is that already established that :caffeine owl:sameAs :theine (doi:10.1002/jlac.18380250106). Cool!