Thursday, December 27, 2018

Creating nanopublications with Groovy

Compound found in Taphrorychus bicolor
Published in Liebigs Annalen, see
this post about the history of that journal.
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).

Second, I now about almost 1200 CCZero nanopublications that tell you in which species a certain metabolite has been found. Sourced from Wikidata, using their SPARQL end point. This collection is a bit boring that this moment, and most of them are human metabolites, where the source is either Recon 2.2 or WikiPathways. But I expect (hope) to see more DOIs to show up. Think We challenge you to reuse Additional Files.

Finally, you are probably interested in learning what one of the created nanopublications looks like, to I put a Gist online: