MetaboLights: Creating the missing Metabolomics community resource

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Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary conditions. It does this by means of spectroscopic and chromatographic techniques and by observing at once not only a few but all compounds visible to the particular technique used. To understand what a change in concentration of one or more of the signals in a spectrum or chromatogram ultimately means, the identity and role of the chemical compounds underlying the respective signal needs to be revealed. This requires curated databases with reference data of chemical structures of biological metabolites assigned to their spectra data. It also requires the knowledge about reference concentrations of metabolites in the biological system of interest under given conditions. In genome and protein science large resources exist to document which genes or proteins are found or expressed under certain conditions in the system of interest. In metabolomics, however, a general system with such information has not yet been instantiated. Instead, a number of resources exist which specialize on certain 'kingdoms of life', species or diseases, or analytical devices. Here, we therefore propose to establish a general metabolomics database resource at the European Binformatics Institute in Hinxton, Cambridge, UK, which serves this crucial information to the biological community in the UK and worldwide. This resource, with the working title 'MetaboLights', will serve information about metabolites and their reference spectra and chromatographic data, their occurrence and concentrations in organisms, tissues, cells, etc, under well-defined conditions, and last but not least documentation about how metabolomics experiments were conducted. Like all other EBI resources, the MetaboLights databases will be completely open to the public, including open access to the data. Data will be made available in publicly accepted open standards. The software will be open source. MetaboLights is not meant to replace specialist resources for Metabolomics. Rather, it will build on prior art and collaborate. We are dedicated to close collaboration with all major parties involved in the creation of this prior art, such as the Metabolomics Society, Metabomeeting and the Metabolomics Standards Initiative. In the molecular biology universe as it exists today, none of the large database efforts, neither in genomics nor any other area, lives an isolated life. Rather, there is a regulated ecosystem of resources, such as GenBank, Ensemble and DDBJ for the genome sciences, which interchange data freely and compete on how to present this data and on its analysis. We aim to come to similar data sharing agreements with major resources such as the Human Metabolome Database, the Golm Metabolome Database or the Rikken Metabolomics Platform. However, MetaboLights will be the first comprehensive, cross-species, cross-technique database which combines curated reference data of pure metabolites, curated information about their occurrence and concentration in species, organs, tissues and cell types under various condition with data characterizing the experiment which lead to these findings.