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          Institute: MPI für molekulare Pflanzenphysiologie     Collection: Publikationen Pflanzenphysiologie     Display Documents



  history
ID: 224175.0, MPI für molekulare Pflanzenphysiologie / Publikationen Pflanzenphysiologie
A proposed framework for the description of plant metabolomics experiments and their results
Authors: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.; Roessner-Tunali, U.; Saito, K.; Smedsgaard, J.; Sumner, L. W.; Wang, T.; Walsh, S.; Wurtele, E. S.; Kell, D. B.
Language:English
Date of Publication (YYYY-MM-DD):2004-12
Title of Journal:Nature Biotechnology
Journal Abbrev.:Nat Biotechnol
Volume:22
Issue / Number:12
Start Page:1601
End Page:1606
Review Status:not specified
Audience:Not Specified
Abstract / Description: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.
Free Keywords:mass-spectrometry
; miame standards
; systems biology
; genomics
; database
; microarray
; identification
; algorithms
; networks
; extracts
External Publication Status:published
Document Type:Article
Communicated by:N. N.
Affiliations:MPI für molekulare Pflanzenphysiologie/Molekulare Physiologie/AG Fiehn
MPI für molekulare Pflanzenphysiologie/Molekulare Physiologie/AG Kopka
External Affiliations:Univ Wales, Dept Comp Sci, Aberystwyth SY23 3DB, Ceredigion, Wales
Univ Wales, Dept Comp Sci, Aberystwyth SY23 3DB, Ceredigion, Wales
Univ Wales, Inst Biol Sci, Aberystwyth SY23 3DB, Ceredigion, Wales
Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany
Univ Manchester, Sch Chem, Manchester M60 1QD, Lancs, England
Plant Res Int, NL-6700 AA Wageningen, Netherlands
Ctr BioSyst Gen, NL-6700 AB Wageningen, Netherlands
AgRes Grasslands Res Ctr, Palmerston North, New Zealand
Washington State Univ, Inst Biol Chem, Pullman, WA 99164 USA
Washington State Univ, Ctr Integrated Biotechnol, Pullman, WA 99164 USA
KRIBB, Plant Cell Biotechnol Lab, Taejon 305600, South Korea
Eugentech Inc, NRL, Taejon 305600, South Korea
Virginia Tech, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA
Iowa State Univ, Dept Biochem Biophys & Mol Biol, WM Keck Metabol Res Lab, Ctr Designer Crops, Ames, IA 50011 USA
Univ Manchester, Sch Biol Sci, Manchester M13 9PL, Lancs, England
Univ Manchester, Dept Comp Sci, Manchester M13 9PL, Lancs, England
Carnegie Inst Washington, Arabidopsis Informat Resource, Dept Plant Biol, Stanford, CA 94305 USA
Univ Melbourne, Sch Bot, Australian Ctr Plant Funct Gen, Parkville, Vic 3010, Australia
Chiba Univ, Grad Sch Pharmaceut Sci, Inage Ku, Chiba 2638522, Japan
Tech Univ Denmark, BioCtr DTU, DK-2800 Lyngby, Denmark
Samuel Roberts Noble Fdn Inc, Ardmore, OK 73401 USA
John Innes Ctr Plant Sci Res, Norwich NR4 7UH, Norfolk, England
Iowa State Univ, Dept Genet Dev & Cell Biol, Ames, IA 50011 USA
Identifiers:ISI:000225638600040 [ID No:1]
ISI:000225638600040 [ID No:2]
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