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

Hélène Ferry-Dumazet1, Laurent Gil1, Catherine Deborde23*, Annick Moing23, Stéphane Bernillon23, Dominique Rolin4, Macha Nikolski5, Antoine de Daruvar15 and Daniel Jacob123

Author Affiliations

1 Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076 Bordeaux, France

2 INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d'Ornon, France

3 Plateforme Métabolome-Fluxome Bordeaux, Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de Bordeaux, BP 81, F-33140 Villenave d'Ornon, France

4 Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d'Ornon, France

5 Université de Bordeaux, Laboratoire Bordelais de Recherche en Informatique, UMR 500, F-33405 Talence, France

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BMC Plant Biology 2011, 11:104  doi:10.1186/1471-2229-11-104

Published: 13 June 2011

Abstract

Background

Improvements 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.

Description

MeRy-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.

Conclusion

MeRy-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 webcite.