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

Helen Jenkins, Nigel Hardy, Manfred Beckmann, John Draper, Aileen R. Smith, Janet Taylor, Oliver Fiehn, Royston Goodacre, Raoul J. Bino, Robert Hall, Joachim Kopka, Geoffrey A. Lane, B. Markus Lange, Jang R. Liu, Pedro Mendes, Basil J. Nikolau, Stephen G. Oliver, Norman W. Paton, Sue Rhee, Ute Roessner-Tunali & 7 others Kazuki Saito, Jørn Smedsgaard, Lloyd W. Sumner, Trevor Wang, Sean Walsh, Eve Syrkin Wurtele, Douglas B. Kell

Research output: Contribution to journalArticle

218 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1601-1606
Number of pages6
JournalNature Biotechnology
Volume22
Issue number12
DOIs
StatePublished - Dec 2004
Externally publishedYes

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Metabolomics
Experiments
Data description
Data handling
Information Storage and Retrieval
Metabolites
Data structures
Data storage equipment
Growth
Chemical analysis
Datasets

ASJC Scopus subject areas

  • Microbiology

Cite this

Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., ... Kell, D. B. (2004). A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology, 22(12), 1601-1606. https://doi.org/10.1038/nbt1041

A proposed framework for the description of plant metabolomics experiments and their results. / Jenkins, Helen; Hardy, Nigel; Beckmann, Manfred; Draper, John; Smith, Aileen R.; Taylor, Janet; Fiehn, Oliver; Goodacre, Royston; Bino, Raoul J.; Hall, Robert; Kopka, Joachim; Lane, Geoffrey A.; Lange, B. Markus; Liu, Jang R.; Mendes, Pedro; Nikolau, Basil J.; Oliver, Stephen G.; Paton, Norman W.; Rhee, Sue; Roessner-Tunali, Ute; Saito, Kazuki; Smedsgaard, Jørn; Sumner, Lloyd W.; Wang, Trevor; Walsh, Sean; Wurtele, Eve Syrkin; Kell, Douglas B.

In: Nature Biotechnology, Vol. 22, No. 12, 12.2004, p. 1601-1606.

Research output: Contribution to journalArticle

Jenkins, H, Hardy, N, Beckmann, M, Draper, J, Smith, AR, Taylor, J, Fiehn, O, Goodacre, R, Bino, RJ, Hall, R, Kopka, J, Lane, GA, Lange, BM, Liu, JR, Mendes, P, Nikolau, BJ, Oliver, SG, Paton, NW, Rhee, S, Roessner-Tunali, U, Saito, K, Smedsgaard, J, Sumner, LW, Wang, T, Walsh, S, Wurtele, ES & Kell, DB 2004, 'A proposed framework for the description of plant metabolomics experiments and their results', Nature Biotechnology, vol. 22, no. 12, pp. 1601-1606. https://doi.org/10.1038/nbt1041
Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J et al. A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology. 2004 Dec;22(12):1601-1606. https://doi.org/10.1038/nbt1041
Jenkins, Helen ; Hardy, Nigel ; Beckmann, Manfred ; Draper, John ; Smith, Aileen R. ; Taylor, Janet ; Fiehn, Oliver ; Goodacre, Royston ; Bino, Raoul J. ; Hall, Robert ; Kopka, Joachim ; Lane, Geoffrey A. ; Lange, B. Markus ; Liu, Jang R. ; Mendes, Pedro ; Nikolau, Basil J. ; Oliver, Stephen G. ; Paton, Norman W. ; Rhee, Sue ; Roessner-Tunali, Ute ; Saito, Kazuki ; Smedsgaard, Jørn ; Sumner, Lloyd W. ; Wang, Trevor ; Walsh, Sean ; Wurtele, Eve Syrkin ; Kell, Douglas B. / A proposed framework for the description of plant metabolomics experiments and their results. In: Nature Biotechnology. 2004 ; Vol. 22, No. 12. pp. 1601-1606.
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