Paper: "Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations"

When I joined the BiGCaT research group in 2012 I was particularly interested in the open science approach of WikiPathways. As a chemist by training and researcher in cheminformatics, metabolites and their metabolic reactions took my particular interest. I am happy that I have been able to fund Denise’s research project. And thanks Denise for this very exciting research. I know it’s just a first step, and far more translational steps are needed, but I for one am very exciting to bridge molecular info to clinical outcomes. 1 minute read

CiTO updates #4: annotations in datasets

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. 3 minute read

Scholia timeline

Sometimes I think back about how Scholia started, and then I think I remember a Twitter discussion. Twitter was a social platform that was unable to fight hate speech. I left it last year in favor of Mastodon. 1 minute read

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