I think that if you want to make your knowledge FAIR, you should use an open license and RDF. Simple. Now, not everything is knowledge. A lot of data is, but a lot more is not, think raw data. Using RDF to explain a protein sequence is still something that makes me feel uneasy. However, first, you need to make RDF, you need to make assumptions explicit, you need to decide on meaning. Making RDF is not easy.

Okay, the Pilot is over ending with 17 papers, 16 of which have CiTO annotations (and so far 4 J.Cheminform. papers after the pilot), but my interest in the Citation Typing Ontology continues and we just need more adoption. Datasets as source of annotations So, here’s a quick Wikidata update.

There are multiple initiatives to support the migration from Twitter to Mastodon (see also this blog post ). But Wikidata should not be forgotten here which has been tracking Mastodon accounts of things in their database: So, here are some Wikidata SPARQL queries to see the uptake: Universities with Mastodon All Mastodon accounts in Wikidata (or subset with also a Twitter account) Nobel Prize winners with Mastodon Academic

Yeah, it has been hard to miss it (see e.g. Should I join Mastodon? A scientists’ guide to Twitter’s rival). Twitter is experiencing some turbulence and Mastodon has become a very attractive, open source, community-driven, inclusive alternative. It’s been around since 2016 and there is some research literature about it already. I got my account in 2018, but did not start actively using it until earlier this year.

In August I reported about 2D depiction of (CX)SMILES in Wikidata via linkouts (going back to 2017). Based on a script by Magnus Manske, I wrote a Wikidata gadget that uses the same CDK Depict (VHP4Safety mirror) to depict the 2D structure in Wikidata itself: Note the depiction of the undefined (CIP) stereochemistry on two atoms. Thanks to Adriano and John for working that out.

Forget the journal impact factor and the H-index. You want your research being used. A first approximation of that is getting cited, sure. So, with the Nobel Prize week over (congrats to all winners! the Neanderthaler prize actually helped my work in Maastricht this week), let’s figure out of you are cited by a Nobel Prize winner.

Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before the start of the pandemic.

I am a bit behind with tweeting about new published papers, but let that not reflect that these papers are not very exciting. The first paper is by Marvin an almost-finished PhD candidate in our group and now working as postdoc on the VHP4Safety project. He has been working on linking adverse outcome pathways (AOPs) with molecular pathways, such as in WikiPathways.

Last month I reported on the start of the NWO Open Science grant and it is time for an update. First, our grant now has a grant number, 203.001.121. For a project that is about identifiers, having a project identifier is a big deal.

Last year, Denise, Tina, Marvin, and I received an NWO Open Science grant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel (see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work part-time on this grant.

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong. Long story short: it worked!