Perspective abstract


Nature Biotechnology 22, 1601 - 1606 (2004)
Published online: 6 December 2004 | doi:10.1038/nbt1041

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

Helen Jenkins1, Nigel Hardy1, Manfred Beckmann2, John Draper2, Aileen R Smith2, Janet Taylor1,21, Oliver Fiehn3, Royston Goodacre4, Raoul J Bino5,6, Robert Hall5, Joachim Kopka3, Geoffrey A Lane7, B Markus Lange8, Jang R Liu9, Pedro Mendes10, Basil J Nikolau11, Stephen G Oliver12, Norman W Paton13, Sue Rhee14, Ute Roessner-Tunali15, Kazuki Saito16, Jørn Smedsgaard17, Lloyd W Sumner18, Trevor Wang19, Sean Walsh19, Eve Syrkin Wurtele20 & Douglas B Kell4


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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  1. Department of Computer Science, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, UK, SY23 3DB.
  2. Institute of Biological Sciences, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, UK, SY23 3DB.
  3. Max Planck Institute of Molecular Plant Physiology, 14424 Potsdam, Germany.
  4. School of Chemistry, The University of Manchester, PO Box 88, Manchester, UK, M60 1QD.
  5. Plant Research International, POB 16, 6700 AA Wageningen, The Netherlands.
  6. Centre for BioSystems Genomics, POB 98, 6700 AB Wageningen.
  7. AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand.
  8. Institute of Biological Chemistry and Center for Integrated Biotechnology, Washington State University, Pullman, Washington 99164-6340, USA.
  9. Plant Cell Biotechnology Laboratory of KRIBB and NRL of Eugentech Inc., PO Box 115, Yuseong, Daejeon, 305-600 Korea.
  10. Virginia Bioinformatics Institute, Virginia Tech, 1880 Pratt Drive, Blacksburg, Virginia 24061, USA.
  11. Center for Designer Crops, W.M. Keck Metabolomics Research Laboratory, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
  12. School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK, M13 9PL.
  13. Department of Computer Science, University of Manchester, Oxford Road, Manchester, UK, M13 9PL.
  14. The Arabidopsis Information Resource, Carnegie Institution of Washington, Department of Plant Biology, 260 Panama Street, Stanford, California 94305, USA.
  15. Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, 3010 Victoria, Australia.
  16. Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan.
  17. Technical University of Denmark, BioCentrum-DTU, Søltofts Plads Building 221, Kgs Lyngby, 2800 Denmark.
  18. The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA.
  19. John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH.
  20. Department of Genetics, Development and Cell Biology, 441 Bessey Hall, Iowa State University, Ames, Iowa 50011, USA.
  21. Present address: IGER, Plas Gogerddan, Aberystwyth, Ceredigion, Wales, UK, SY23 3EB.

Correspondence to: Nigel Hardy1 e-mail: nwh@aber.ac.uk



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