MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

BMC Plant Biology

Database

Catherine Deborde¹  Annick Moing¹  Stéphane Bernillon¹  Hélène Ferry-Dumazet²  Laurent Gil²  Daniel Jacob³  Antoine de Daruvar⁴  Macha Nikolski⁵  Dominique Rolin⁶ 

[1] INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140, Villenave, d'Ornon, France;Plateforme Métabolome-Fluxome Bordeaux, Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de Bordeaux BP 81, F-33140, Villenave, d'Ornon, France;Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076, Bordeaux, France;Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076, Bordeaux, France;INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140, Villenave, d'Ornon, France;Plateforme Métabolome-Fluxome Bordeaux, Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de Bordeaux BP 81, F-33140, Villenave, d'Ornon, France;Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076, Bordeaux, France;Université de Bordeaux, Laboratoire Bordelais de Recherche en Informatique, UMR 500, F-33405, Talence, France;Université de Bordeaux, Laboratoire Bordelais de Recherche en Informatique, UMR 500, F-33405, Talence, France;Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140, Villenave, d'Ornon, France;

关键词: Nuclear Magnetic Resonance;    Nuclear Magnetic Resonance Spectrum;    Metabolite Identification;    Trigonelline;    Metabolomics Experiment;   

DOI  :  10.1186/1471-2229-11-104

 received in 2010-12-17, accepted in 2011-06-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundImprovements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments.DescriptionMeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues.ConclusionMeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

【 授权许可】

Unknown   
© Ferry-Dumazet et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.