Sunday, October 08, 2017

CDK used in SIRIUS 3: metabolomics tools from Germany

Screenshot from the SIRIUS 3 Documentation.
License: unknown.
It has been ages I blogged about work I heard about and think should receive more attention. So, I'll try to pick up that habit again.

After my PhD research (about machine learning (chemometrics, mostly), crystallography, QSAR) I first went into the field metabolomics. Because is combines core chemistry with the complexity biology. My first position was with Chris Steinbeck, in Cologne, within the bioinformatics institute led by Prof. Schomburg (of the BRENDA database). During that year, I worked in a group that worked on NMR data (NMRShiftDb, dr. Stefan Kuhn), Bioclipse (collaboration with Ola Spjuth), and, of course, the Chemistry Development Kit (see our new paper).

This new paper, actually, introduces functionality that was developed in that year, for example, work started by Miquel Rojas-Cheró. This includes the work on atom types, which we needed to handle radicals, lone pairs, etc, for delocalisation. It also includes work around handling molecular formula and calculating molecular formulas from (accurate) molecular masses. For the latter, more recent work even further improved on earlier work.

So, whenever metabolomics work is published and they use the CDK, I realize that what the CDK does has impact. This week Google Scholar alerted me about a user guidance document for SIRIUS 3 (see the screenshot). Seems really nice (great) work from Sebastian Böcker et al.!

It also makes me happy, as our Faculty of Heath, Medicine, and Life Sciences (FHML) is now part of the Netherlands Metabolomics Center, and that we published the recent article our vision of a stronger, more FAIR European metabolomics community.