Establishing reporting standards for metabolomic and metabonomic studies: A call for participation

被引:72
作者
Fiehn, Oliver
Kristal, Bruce
Van Ommen, Ben
Sumner, Lloyd W.
Sansone, Susanna-Assunta
Taylor, Chris
Hardy, Nigel
Kaddurah-Daouk, Rima
机构
[1] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA
[2] Burke Rehabil Hosp, White Plains, NY USA
[3] TNO, Nutr & Food Res, Zeist, Netherlands
[4] Samuel Roberts Noble Fdn Inc, Ardmore, OK USA
[5] European Bioinformat Inst, EMBL Outstn, Cambridge, England
[6] Univ Wales, Dept Comp Sci, Aberystwyth, Dyfed, Wales
[7] Duke Univ, Med Ctr, Dept Psychiat & Behav Sci, Durham, NC USA
关键词
D O I
10.1089/omi.2006.10.158
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular regulation, resulting in the visible phenotypes. Therefore, the comprehensive analysis of metabolite levels and fluxes renders a suitable tool for assessing the degree of perturbation in biological systems. Lessons derived from development of other OMICS areas (genomics, proteomics, and transcriptomics) have shown that large-scale comparisons and interpretations will require the re-use of data over long periods of time and by multiple laboratories with different expertise and backgrounds. Reaching this goal will require standardization of reporting structures of metabolomic studies for journal publication purposes, for regulatory deposition, and for database dissemination. An initiative by the Metabolomics Society is presented that aims to define important aspects of metabolomic workflows. These include biological study designs, chemical analysis, and data processing, as well as the ontologies that are necessary in this framework. This paper is part of the special issue of OMICS on data standards.
引用
收藏
页码:158 / 163
页数:6
相关论文
共 15 条
[1]   Potential of metabolomics as a functional genomics tool [J].
Bino, RJ ;
Hall, RD ;
Fiehn, O ;
Kopka, J ;
Saito, K ;
Draper, J ;
Nikolau, BJ ;
Mendes, P ;
Roessner-Tunali, U ;
Beale, MH ;
Trethewey, RN ;
Lange, BM ;
Wurtele, ES ;
Sumner, LW .
TRENDS IN PLANT SCIENCE, 2004, 9 (09) :418-425
[2]  
*CCPN, 2006, COLL COMP PROJ NMR C
[3]   Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks [J].
Fiehn, O .
COMPARATIVE AND FUNCTIONAL GENOMICS, 2001, 2 (03) :155-168
[4]   A proposed framework for the description of plant metabolomics experiments and their results [J].
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 .
NATURE BIOTECHNOLOGY, 2004, 22 (12) :1601-1606
[5]   Summary recommendations for standardization and reporting of metabolic analyses [J].
Lindon, JC ;
Nicholson, JK ;
Holmes, E ;
Keun, HC ;
Craig, A ;
Pearce, JTM ;
Bruce, SJ ;
Hardy, N ;
Sansone, SA ;
Antti, H ;
Jonsson, P ;
Daykin, C ;
Navarange, M ;
Beger, RD ;
Verheij, ER ;
Amberg, A ;
Baunsgaard, D ;
Cantor, GH ;
Lehman-McKeeman, L ;
Earll, M ;
Wold, S ;
Johansson, E ;
Haselden, JN ;
Kramer, K ;
Thomas, C ;
Lindberg, J ;
Schuppe-Koistinen, I ;
Wilson, ID ;
Reily, MD ;
Robertson, DG ;
Senn, H ;
Krotzky, A ;
Kochhar, S ;
Powell, J ;
van der Ouderaa, F ;
Plumb, R ;
Schaefer, H ;
Spraul, M .
NATURE BIOTECHNOLOGY, 2005, 23 (07) :833-838
[6]   So whats the deal with metabonomics? Metabonomics measures the fingerprint of biochemical perturbations caused by disease, drugs, and toxins [J].
Lindon, JC ;
Holmes, E ;
Nicholson, JK .
ANALYTICAL CHEMISTRY, 2003, 75 (17) :384A-391A
[7]  
*MET, 2005, MET 1 0 C
[8]  
*MET SOC, 2005, MISS STAT
[9]  
*MET SOC, 2005, OV COMM REP STAND
[10]  
*NIH, 2005, NAT I HLTH MET WORKS