Publishing habits changes very slowly, too slowly. The whole industry is incredibly inert, which can lead to severe frustration as it did for me. But sometimes small changes can do so much.
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 dead
Last week the third paper got published in the Citation Typing Ontology Collection and this weekend I finished adding the citation annotations to Wikidata. While the number of papers in the Journal of Cheminformatics is only slowly growing, the number of journals receiving annotated citations is growing faster. And there are 70 now: The Scholia patch needed for this updated table is not online yet.
During the time of the editorial about the Journal of Cheminformatics Citation Typing Ontology (CiTO) Pilot I already worked out a model to add CiTO annotation in Wikidata. It looks like this for the first research article with annotation: At the time I also write some SPARQL queries against Wikidata to summaries the current use.
WP4846 that I started on March 16. It will see a massive overhaul in the next weeks. Voices are getting stronger over how important Open Science is. Insiders have known the advantages for decades. We also know the issues in the transition, but the transition has been steady.
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.
Twitter profile. It giet oan! That it a Frisian phrase for something unlike is going to happen, like and particularly related to the Elfstedentocht. ChemCuration 2019 is a go. The website is online, the Twitter account and hashtag are ready, we got a poster prize, and here is the call for posters!
Glucuronide functional group. Now that the ChemCuration 2019 online poster conference is nearing, and my upcoming talks about chemistry in Wikidata (also needing curation), and the much longer process of curation of metabolite (-like) structures in WikiPathways, I decided that something I tweeted earlier this week is actually quite useful, and therefore something I should really write up in my lab notebook.
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.