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.

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 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.

Screenshot of the Open Science History group on CiteULike. Open Science has been around for some time. Before Copyright became a thing, knowledge dissemination was mostly limited by how easy you could get knowledge from one place to another. The introduction of Copyright changed this.

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.

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. On the right, a depiction is given of a compound found in Taphrorychus bicolor (doi:10.1002/JLAC.199619961005). Published in Liebigs Annalen , see this post about the history of that journal. There are two good things about this.

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.

Found my way back to my room a few kilometers from the San Francisco city center, after a third day at the WikiPathways 2018 Summit at the Gladstone Institutes in Mission Bay, celebrating 10 years of the project, which I only joined some six and a half years ago. The Summit was awesome and the whole trip was awesome. The flight was long, with a stop in Seattle.

There was a lot of Open Science news this week. The announcement of the Google Dataset Search was one of them: Of course, I first tried searching for “RDF chemistry” which shows some of my data sets (and a lot more): It picks up data from many sources, such as Figshare in this image. That means it also works (well, sort of, as Noel O’Boyle noticed) for supplementary information from the Journal of Cheminformatics.

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.

The U.S.A and European nanosafety communities have a longstanding history of collaboration. On both sides there are working groups, NanoWG and WG-F (previously called WG4) of the NanoSafety Cluster. I have been chair of WG4 for about three years and still active in the group, though in the past half year, without dedicated funding, less active. That is already changing again with the imminent start of the NanoCommons project.