An email which I’m delighted to blog. [from WP: Metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind” – specifically, the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression.]
my postdoctoral scientist Dr Tobias Kind has alerted me that you have been giving a lecture during the Open Repositories 2008 conference, and that you had asked the larger community for examples.
We just wanted to let you know (i.e. for mere information to you, no action requested), we are a rather small lab but have big ambitions to make (‘all’) our data publicly available, at least those that were or are about to be published and/or for which our collaborators have
granted permission to publish the data (and metadata).
If interested, please find below a link to our public studies that are composed of experimental design metadata as well as processed metabolite data and the underlying unprocessed data files. So, in principle, anyone could download our data and prove us wrong (or hopefully, concur with our findings), and we hope that our repositories (SetupX and BinBase) will become a helpful tool for researchers in the area.
Our publications on the databases and on structure elucidation are
found on http://fiehnlab.ucdavis.edu/publications/
An example of a study that is compliant with the ‘Metabolomics Standards Initiative’ is published in Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau BJ (2008) Quality control for plant metabolomics: Reporting MSI-compliant studies.
Journal 53, 691-704
And the data for this study are obviously public at
We will publish our source codes, documentation and help files for installations for the databases within the next 4-8 weeks. Snippets of these are found under the pages of my staff, i.e.
Gert Wohlgemuth, http://fiehnlab.ucdavis.edu/staff/wohlgemuth/binbase/
Martin Scholz http://fiehnlab.ucdavis.edu/staff/scholz/dev/
Tobias Kind http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/ (e.g.
the Seven Golden Rules)
Oliver Fiehn, Assoc. Prof. MCB
– Metabolomics –
UC Davis Genome Center
GBSF Building room 1315
451 East Health Sciences Drive
Davis (CA) 95616-8816
ofiehn AT ucdavis DOT edu
PMR: This is great. The data are both numerous and complex so making them available will be very valuable to other labs doing the same sort of work. And they shouldn’t worry about being a small lab – most labs belong to the “long tail” of science.
FWIW Scientific American carried an article this month about Science 2.0 with contribtuions from Open Wet Ware, Jean-Claude Bradley, Cameron Neylon, etc. I thought it was a balanced coverage of the pluses and minuses of Open Notebook Science and related efforts