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 (1)H-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.
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 (1)H-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.
Authors: V Neveu; J Perez-Jiménez; F Vos; V Crespy; L du Chaffaut; L Mennen; C Knox; R Eisner; J Cruz; D Wishart; A Scalbert Journal: Database (Oxford) Date: 2010-01-08 Impact factor: 3.451
Authors: David S Wishart; Dan Tzur; Craig Knox; Roman Eisner; An Chi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; Mike Lewis; Marie-Aude Coutouly; Ian Forsythe; Peter Tang; Savita Shrivastava; Kevin Jeroncic; Paul Stothard; Godwin Amegbey; David Block; David D Hau; James Wagner; Jessica Miniaci; Melisa Clements; Mulu Gebremedhin; Natalie Guo; Ying Zhang; Gavin E Duggan; Glen D Macinnis; Alim M Weljie; Reza Dowlatabadi; Fiona Bamforth; Derrick Clive; Russ Greiner; Liang Li; Tom Marrie; Brian D Sykes; Hans J Vogel; Lori Querengesser Journal: Nucleic Acids Res Date: 2007-01 Impact factor: 16.971
Authors: Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R Jones; Pierre-Alain Binz; Eric W Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra Orchard; Juan Antonio Vizcaíno; Henning Hermjakob; Christian Stephan; Helmut E Meyer; Martin Eisenacher Journal: Database (Oxford) Date: 2013-03-12 Impact factor: 3.451
Authors: Jianguo Xia; Rupasri Mandal; Igor V Sinelnikov; David Broadhurst; David S Wishart Journal: Nucleic Acids Res Date: 2012-05-02 Impact factor: 16.971
Authors: Reza M Salek; Steffen Neumann; Daniel Schober; Jan Hummel; Kenny Billiau; Joachim Kopka; Elon Correa; Theo Reijmers; Antonio Rosato; Leonardo Tenori; Paola Turano; Silvia Marin; Catherine Deborde; Daniel Jacob; Dominique Rolin; Benjamin Dartigues; Pablo Conesa; Kenneth Haug; Philippe Rocca-Serra; Steve O'Hagan; Jie Hao; Michael van Vliet; Marko Sysi-Aho; Christian Ludwig; Jildau Bouwman; Marta Cascante; Timothy Ebbels; Julian L Griffin; Annick Moing; Macha Nikolski; Matej Oresic; Susanna-Assunta Sansone; Mark R Viant; Royston Goodacre; Ulrich L Günther; Thomas Hankemeier; Claudio Luchinat; Dirk Walther; Christoph Steinbeck Journal: Metabolomics Date: 2015-05-26 Impact factor: 4.290