Bioclipse git experiences #1: Strip away unwanted plugins

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another. A second use case can be a file that must be removed (there are valid reasons for that). Because these posts are based on Bioclipse work, there will be some specific terminology, but the approach I regularly apply in other situations. 1 minute read

new paper: "Wikidata as a knowledge graph for the life sciences"

A figure from the article, outlining the idea of using SPARQL queries to extract data from the open knowledge base. As a reader of my blog, you know I have been doing quite some research where Wikidata has some role. I am preparing a paper on the work I have done around chemicals in Wikidata, based on what I presented at the ICCS with a poster. So, I was delighted when Andra and Andrew asked me to contribute to a paper outline the importance of Wikidata to the life sciences. The paper was published in eLife, which I’m excited about to, as they do a significant amount of publishing innovation. less than 1 minute read

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

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