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; Kazuki Saito; Jørn Smedsgaard; Lloyd W. Sumner; Trevor Wang; Sean Walsh; Eve Syrkin Wurtele; Douglas B. Kell

doi:10.1038/nbt1041

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-TunaliKazuki Saito, Jørn Smedsgaard, Lloyd W. Sumner, Trevor Wang, Sean Walsh, Eve Syrkin Wurtele, Douglas B. Kell

Research output: Contribution to journal › Article › 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
Pages (from-to)	1601-1606
Number of pages	5
Journal	Nature biotechnology
Volume	22
Issue number	12
DOIs	https://doi.org/10.1038/nbt1041
Publication status	Published - Dec 2004

Keywords

Information systems (data; proposed framework for description of plant metabolomics expts. and their results); Bioinformatics (plant metabolomics; proposed framework for description of plant metabolomics expts. and their results); Embryophyta; Internet; Metabolism (proposed framework for description of plant metabolomics expts. and their results); Information systems (storage; proposed framework for description of plant metabolomics expts. and their results)

Research Beacons, Institutes and Platforms

Manchester Institute of Biotechnology

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10.1038/nbt1041

Cite this

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.",

keywords = "Information systems (data; proposed framework for description of plant metabolomics expts. and their results); Bioinformatics (plant metabolomics; proposed framework for description of plant metabolomics expts. and their results); Embryophyta; Internet; Metabolism (proposed framework for description of plant metabolomics expts. and their results); Information systems (storage; proposed framework for description of plant metabolomics expts. and their results)",

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

year = "2004",

month = dec,

doi = "10.1038/nbt1041",

language = "English",

volume = "22",

pages = "1601--1606",

journal = "Nature biotechnology",

issn = "1546-1696",

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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, Helen

AU - Hardy, Nigel

AU - Beckmann, Manfred

AU - Draper, John

AU - Smith, Aileen R.

AU - Taylor, Janet

AU - Fiehn, Oliver

AU - Goodacre, Royston

AU - Bino, Raoul J.

AU - Hall, Robert

AU - Kopka, Joachim

AU - Lane, Geoffrey A.

AU - Lange, B. Markus

AU - Liu, Jang R.

AU - Mendes, Pedro

AU - Nikolau, Basil J.

AU - Oliver, Stephen G.

AU - Paton, Norman W.

AU - Rhee, Sue

AU - Roessner-Tunali, Ute

AU - Saito, Kazuki

AU - Smedsgaard, Jørn

AU - Sumner, Lloyd W.

AU - Wang, Trevor

AU - Walsh, Sean

AU - Wurtele, Eve Syrkin

AU - Kell, Douglas B.

PY - 2004/12

Y1 - 2004/12

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.

KW - Information systems (data; proposed framework for description of plant metabolomics expts. and their results); Bioinformatics (plant metabolomics; proposed framework for description of plant metabolomics expts. and their results); Embryophyta; Internet; M

U2 - 10.1038/nbt1041

DO - 10.1038/nbt1041

M3 - Article

C2 - 15583675

SN - 1546-1696

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

Keywords

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