Conflict of Interest. Or why I am stepping down as Editor-in-Chief of the Journal of Cheminformatics.

Rough timeline of the Journal of Cheminformatics. The linked PDF has linked years with references. In this open letter, I will explain why I intend to step down as Editor-in-Chief of the Journal of Cheminformatics, which also happens to be a Springer Nature journal. It took me two years to come to this decision, and it cannot be claimed that I did not carefully evaluate the various aspects of it. However, I have now come to the conclusion that the opportunity it gives me to implement my ambition to shape open science chemistry now conflicts with the interests of Springer Nature. I will here outline some of the things I have taken into consideration. 1 minute read

Downloading all currently released BridgeDb identifier mapping databases

The BridgeDb project (doi:10.1186/1471-2105-11-5) (and ELIXIR recommended interoperability resource) has several aims, all around identifier mapping: 2 minute read

CiTO updates #3: third paper in the collection and updated Scholia patch

Last week the third paper got published in the Citation Typing Ontology Collection and this weekend I finished adding the citation annotations to Wikidata. less than 1 minute read

new paper: "WikiPathways: connecting communities"

The number of revisions and contributors for all pathways in the human pathway analysis collection. less than 1 minute read

CiTO updates #2: annotation migration to Wikidata and first Scholia patch

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 : 1 minute read

CiTO updates #1: first research paper in the Journal of Cheminformatics with CiTO annotation published

After a time of exploration of technical needs, idea, plans, the Journal of Cheminformatics launched its Citation Typing Ontology (CiTO) Pilot this summer (doi:10.1186/s13321-020-00448-1). I am very excited about this, because the CiTO tells us why we are citing literature. We are a very long way away from publishing industry adoption, but we have to start somewhere. Laeeq Ahmed et al. published a few weeks ago the first research article with CiTO annotation of references (“Predicting target profiles with confidence as a service using docking scores”)! less than 1 minute read

SARS-CoV-2, COVID-19, and Open Science

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. Contributing to Open Science is simple: there are plenty of project where you can contribute without jeopardizing your own research (funding or prestige). Myself, my small contributions have been done without funding too. But I needed to do something. I have been mostly self-quarantined since March 6, with only very few exception. And I’m so done with it. Like so many other people. It won’t stop me wearing masks when I go shopping (etc). 6 minute read