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A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."

Julian L Griffin1234*, Helen J Atherton12, Christoph Steinbeck5 and Reza M Salek125

Author Affiliations

1 MRC Human Nutrition Research, Elsie Widdowson Laboratory, Fulbourn Road, Cambridge, CB1 9NL, UK

2 The Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge CB2 1GA, UK

3 The Cambridge Systems Biology Centre, Tennis Court Road, University of Cambridge, Cambridge CB2 1GA, UK

4 The MRC Centre for Obesity and Related Diseases (MRC CORD), the University of Cambridge Metabolic Research Laboratories, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK

5 The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

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BMC Research Notes 2011, 4:272  doi:10.1186/1756-0500-4-272

Published: 29 July 2011

Abstract

Background

Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment.

Findings

In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data.

Conclusions

The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers.

Keywords:
data standards; metabolomics repository; bioinformatics; NMR spectroscopy