MetaboLights: towards a new COSMOS of metabolomics data management

Metabolomics, Oct 2012

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://​www.​ebi.​ac.​uk/​metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6–8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

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MetaboLights: towards a new COSMOS of metabolomics data management

Christoph Steinbeck 0 1 2 3 Pablo Conesa 0 1 2 3 Kenneth Haug 0 1 2 3 Tejasvi Mahendraker 0 1 2 3 Mark Williams 0 1 2 3 Eamonn Maguire 0 1 2 3 Philippe Rocca-Serra 0 1 2 3 Susanna-Assunta Sansone 0 1 2 3 Reza M. Salek 0 1 2 3 Julian L. Griffin 0 1 2 3 0 R. M. Salek J. L. Griffin Elsie Widdowson Laboratory , Fulbourn Road, Cambridge CB1 9NL, UK 1 E. Maguire P. Rocca-Serra S.-A. Sansone Oxford e-Research Centre, University of Oxford , Oxford, UK 2 C. Steinbeck (&) P. Conesa K. Haug T. Mahendraker M. Williams European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK 3 R. M. Salek J. L. Griffin Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, UK Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics. 1 Introduction Metabolomics has become an important phenotyping technique for molecular biology and medicine. It assesses the molecular state of an organism or collections of organisms through the comprehensive quantitative and qualitative analysis of all small molecules in cells, tissues, and body fluids. Metabolic processes are at the core of physiology. Consequently, metabolomics is ideally suited as a medical tool to characterize disease states in organisms, as a tool for assessment of organisms for their suitability in, for example, renewable energy production, or for biotechnological applications in general. In addition application of metabolomics in environmental science, toxicology, food and medical industry is well established, growing and documented. Metabolomics studies generate large amounts of analytical data (Giga- to Terabytes depending on the size of the study) and therefore impose significant challenges for biomedical and life science e-infrastructures to cope with such data volumes and ensure that the data are captured, stored and disseminated based on open and widely accepted community standards. Years after the first standardisation exercises (Fiehn et al. 2007; Taylor et al. 2008), metabolomics is now reaching the state of a mature analytical technique as indicated by the establishment of 68 Regional Comprehensive Metabolomics Resource Cores (RCMRCs) by the NIH in the United States (http://grants.nih.gov/grants/guide/ rfa-files/RFA-RM-11-016.html). In addition, we are now facing a rich ecosystem of specialised metabolomics databases, such as (Wishart et al. 2007; Kopka et al. 2005; Smith et al. 2005; Skogerson et al. 2011) as well as the first general metabolomics repositories (http://www.ebi.ac.uk/ metabolights) and databases emerging. In Europe, the COSMOS consortium of 14 leading laboratories in metabolomics will begin its work on standards, data management and dissemination in metabolomics. Here, we outline these developments and show how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics. 2 MetaboLights: a cross-species repository for metabolomics experiments The European Bioinformatics Institute (EMBL-EBI) has recently launched MetaboLights, a database for metabolomics experiments and the associated metadata. It aims to become the first comprehensive, cross-species, crossplatform metabolomics database maintained by one of the major open access data providers in molecular biology. The EBI ensures long-term stability and maintenance of the resource. Deposited datasets are assigned a stable identifier of the form MTBLS1 (the first dataset ever deposited in MetaboLights). These identifiers, like other stable identifiers in bioinformatics, can be used to mark datasets in publications or merge data in systems biology applications. Fig. 2 MetaboLights data submission workflow Fig. 1 MetaboLights general outline with repository and reference layer. The reference layer is work currently in progress Like all other EBI resources (...truncated)


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Christoph Steinbeck, Pablo Conesa, Kenneth Haug, Tejasvi Mahendraker, Mark Williams, Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Reza M. Salek, Julian L. Griffin. MetaboLights: towards a new COSMOS of metabolomics data management, Metabolomics, 2012, pp. 757-760, Volume 8, Issue 5, DOI: 10.1007/s11306-012-0462-0