What metabolites are found in which species? Nanopublications from Wikidata

In December I reported about Groovy code to create nanopublications . This has been running for some time now, extracting nanopubs that assert that some metabolite is found in some species. I send the resulting nanopubs to Tobias Kuhn , to populate his Growing Resource of Provenance-Centric Scientific Linked Data (doi:10.1109/eScience.2018.00024, PDF). less than 1 minute read

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

Two presentations at WikiPathways 2018 Summit #WP18Summit

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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