Doing the "Open Science Challenge"

Screenshot of the sign up page. Triggered by the “reflections on your career” in the announcement I decide to give the Open Science Challenge by Heidi Seibold a try: “12 emails over the course of a month that are designed to help you on your Open Science journey.” less than 1 minute read

Finding Mastodon accounts with Wikidata (a few SPARQL queries)

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: less than 1 minute read

Wikidata script for SMILES, SMARTS, and CXSMILES depiction

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: less than 1 minute read

s/Twitter/Mastodon/g

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. 1 minute read

Is your research cited by a Nobel prize winner?

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. Wikidata allows us to figure this out with a SPARQL query (created together with Adriano): 1 minute read

Wikidata now escapes SMILES and CXSMILES!

In the end it was a very simple change today (huge thanks to Nikki!), but Wikidata now escapes SMILES and CXSMILES (P10718) with the formatter URL (P1630)! less than 1 minute read

Biology, ACPs, lipids, cheminformatics, and Dagstuhl

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. The first I attended the Computational Metabolomics meeting, with the focus From Cheminformatics to Machine Learning, one of the things we concerned ourselves with was how to do computation with compound classes (see Section 3.6 and this online book). We know how to handle SMILES and we know how to the substructure searching with SMARTS, but what if you have compound classes or lipid classes? Biology is a greasy business. 1 minute read