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. 1 minute read

Join me in encouraging the ACS to join the Initiative for Open Citations

My research is into abstract representation of chemical information, important for other research to be performed. Indeed, my work is generally reused, but knowing which research fields my work is used in, or which societal problems it is helping solve, is not easily retrieved or determined. Efforts like WikiCite and Scholia do allow me to navigate the citation network, so that I can determine which research fields my output influences and which diseases are studied with methods I proposed. Here’s a network of topics of articles citing my work: 1 minute read

Programming in the Life Sciences #23: research output for the future

A random public domain picture with 10 in it. Ensuring that you and others can understand you research output five years from now requires effort. This is why scholars tend to keep lab notebooks. The computational age has perhaps made us a bit lazy here, but we still make an effort. A series of Ten Simple Rules articles outline some of the things to think about: 1 minute read

Two presentations at WikiPathways 2018 Summit #WP18Summit

2 minute read

Data Curation: 5% inspiration, 95% frustration (cleaning up data inconsistencies)

Slice of the spreadsheet in the supplementary info. 2 minute read

Also new this week: "Google Dataset Search"

There was a lot of Open Science news this week. The announcement of the Google Dataset Search was one of them: 1 minute read

Compound (class) identifiers in Wikidata

Bar chart showing the number of compounds with a particular chemical identifier. I think Wikidata is a groundbreaking project, which will have a major impact on science. One of the reasons is the open license (CCZero), the very basic approach (Wikibase), and the superb community around it. For example, setting up your own Wikibase including a cool SPARQL endpoint, is easily done with Docker. 3 minute read