The BridgeDb project (doi:10.1186/1471-2105-11-5) (and ELIXIR recommended interoperability resource) has several aims, all around identifier mapping: provide a Java API for identifier mapping provide ID mappings (two flavors: with and without semantic meaning) provide services (R package, OpenAPI webservice) track the history of identifiers The last one is more recent and two aspects are under development here: secondary identifiers and

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.

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.

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.

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.

Hi all, welcome to this winter solstice challenge! Umm, to not give our southern hemisphere colleagues not a disadvantage, as their winter solstice has already passes, you’re up for a summer solstice challenge! Introduction So, you know ImpactStory and Altmetric.com (if not, browse my blog); these are wonderful tools to see what people are doing with your work.

It takes effort to move scholarly publishing forward. And the traditional publishers have not all shown to be good at that: we’re still basically stuck with machine-broken channels like PDFs and ReadCubes. They seem to all love text mining, but only if they can do it themselves. Fortunately, there are plenty of people who do like to make a difference and like to innovate. I find this important, because if we do not do it, who will.

SWAT4LS was once again a great meeting. I doubt I will find time soon enough to write up notes, but at least I can post the eNanoMapper poster I presented, which is available from F1000Research: