chem-bla-ics: December 2018

Replacing BibTeX with Citation.js

As part of replacing LaTeX with Markdown for my Groovy Cheminformatics book (now Open Access), I also needed to replace BibTex. Fortunately, Citation.js supports Wikidata and the solution by Lars was simpler than I hoped. Similar to LaTeX, I have citations annotated in the Markdown, but the reference code does not refer to a BibTeX file entry, but to Wikidata (see also Wikidata-powered citation lists with citation.js).

Dec

Creating nanopublications with Groovy

Yesterday I struggled some with creating nanopublications with Groovy. My first attempt was an utter failure, but then I discovered Thomas Kuhn's NanopubCreator and it was downhill from there.

There are two good things about this. First, I now have a code base that I can easily repurpose to make trusty nanopublications (doi:10.1007/978-3-319-07443-6_63) about anything structured as a table (so can you).

Dec

Groovy Cheminformatics rises from the ashes

Like a phoenix (Phenix aegyptus), my Groovy Cheminformatics rises from the ashes. About a year ago I blogged that I could not longer maintain my book, not in the print form. The hardest part was actually resizing the cover each time the book got thicker. I actually started the book about 10 years ago, but the wish to make it Open Access grew bigger with the years.

So, here we go. It's based on CDK 2.0, but somewhere in the coming weeks I'll migrate to the latest version.

Dec

About Frontiers

Frontiers is getting a lot of critique at this moment, about very low rejection rates (only ~10%), reviewers who seemingly cannot reject articles, the use of the impact factor (sad), their almost pyramid-like gaming of recruiting editors, reviewers, etc are questionable to me (focused on continuous growth of literature, which we must not want), and perhaps most important, questionable lobbying around Plan S. Also, they are just expensive and I see little real publishing innovation.

Dec

New paper: "Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials"

Marvin Martens published his vision on the integration of adverse outcome with biological pathways (doi:10.3389/fgene.2018.00661). Specifically, he looked into our options to link the AOPWiki with WikiPathways, taking input from various people around the world (see the list of co-authors).

Dec

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

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.