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

H. Jenkins; N. Hardy; M- Beckmann; J. Draper; A.R. Smith; J. Taylor; O. Fiehn; R. Goodacre; R.J. Bino; R. Hall; J. Kopka; G.A. Lane; B.M. Lange; J.R. Liu; P. Mendes; B.J. Nikolau; S.G. Oliver; N.W. Paton; S. Rhee; U. Roessner-Tunali; K. Saito; Jørn Smedsgaard; L.W. Sumner; T. Wang; S. Walsh; E.S. Wurtele; D.B. Kell

doi:10.1038/nbt1041

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

H. Jenkins, N. Hardy, M- Beckmann, J. Draper, A.R. Smith, J. Taylor, O. Fiehn, R. Goodacre, R.J. Bino, R. Hall, J. Kopka, G.A. Lane, B.M. Lange, J.R. Liu, P. Mendes, B.J. Nikolau, S.G. Oliver, N.W. Paton, S. Rhee, U. Roessner-TunaliK. Saito, Jørn Smedsgaard, L.W. Sumner, T. Wang, S. Walsh, E.S. Wurtele, D.B. Kell

Research output: Contribution to journal › Journal article › Research › peer-review

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 language	English
Journal	Nature Biotechnology
Volume	22
Issue number	12
Pages (from-to)	1601-1606
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt1041
Publication status	Published - 2004

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Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R., Kopka, J., Lane, G. A., Lange, B. M., Liu, J. R., Mendes, P., Nikolau, B. J., Oliver, S. G., Paton, N. W., Rhee, S., ... 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

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title = "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.",

author = "H. Jenkins and N. Hardy and M- Beckmann and J. Draper and A.R. Smith and J. Taylor and O. Fiehn and R. Goodacre and R.J. Bino and R. Hall and J. Kopka and G.A. Lane and B.M. Lange and J.R. Liu and P. Mendes and B.J. Nikolau and S.G. Oliver and N.W. Paton and S. Rhee and U. Roessner-Tunali and K. Saito and J{\o}rn Smedsgaard and L.W. Sumner and T. Wang and S. Walsh and E.S. Wurtele and D.B. Kell",

year = "2004",

doi = "10.1038/nbt1041",

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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

TY - JOUR

T1 - A proposed framework for the description of plant metabolomics experiments and their results

AU - Jenkins, H.

AU - Hardy, N.

AU - Beckmann, M-

AU - Draper, J.

AU - Smith, A.R.

AU - Taylor, J.

AU - Fiehn, O.

AU - Goodacre, R.

AU - Bino, R.J.

AU - Hall, R.

AU - Kopka, J.

AU - Lane, G.A.

AU - Lange, B.M.

AU - Liu, J.R.

AU - Mendes, P.

AU - Nikolau, B.J.

AU - Oliver, S.G.

AU - Paton, N.W.

AU - Rhee, S.

AU - Roessner-Tunali, U.

AU - Saito, K.

AU - Smedsgaard, Jørn

AU - Sumner, L.W.

AU - Wang, T.

AU - Walsh, S.

AU - Wurtele, E.S.

AU - Kell, D.B.

PY - 2004

Y1 - 2004

N2 - 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.

AB - 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.

U2 - 10.1038/nbt1041

DO - 10.1038/nbt1041

M3 - Journal article

C2 - 15583675

SN - 1087-0156

VL - 22

SP - 1601

EP - 1606

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 12

ER -

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

Abstract

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