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A proposed framework for the description of plant metabolomics experiments and their results

Abstract

The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http://www.armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data.

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Acknowledgements

The authors gratefully acknowledge the United Kingdom Food Standards Agency (under the G02006 project), the United Kingdom Biotechnology and Biological Sciences Research Council (particularly under the HiMet project) and the United Kingdom Engineering and Physical Sciences Research Council for support of their work in metabolomics. We would also like to thank personnel at the United Kingdom Institute of Grassland and Environmental Research and delegates at the 1st, 2nd and 3rd International Plant Metabolomics Conferences for many useful discussions.

Author information

Correspondence to Nigel Hardy.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Notes 'ArMet design' (ZIP 171 kb)

Supplementary Notes 'Controlled vocabulary samples' (PDF 127 kb)

Supplementary Notes 'ArMet subcomponent design: GC-MS' (PDF 143 kb)

Supplementary Notes 'ArMet example customization' (PDF 221 kb)

Supplementary Notes 'ArMet design SQL' (ZIP 3 kb)

Supplementary Notes 'ArMet core XML' (ZIP 19 kb)

Supplementary Notes 'ArMet on-line forms access' (PDF 163 kb)

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Further reading

Figure 1: The nine ArMet components and their interdependencies describing the key concepts of a metabolomics experiment modeled using standard UML packages.

Bob Crimi

Figure 2: ArMet core components and detailed subcomponents.

Bob Crimi

Figure 3: The 'MetabolomeEstimate' component.

Bob Crimi