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, cross-platform 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.
Like all other EBI resources, the MetaboLights database is completely open to the public, including open access to the data. Data are made available in publicly accepted open standards compliant with community standards (BioSharing: http://biosharing.org/standards_view
), including Minimum Information for Biological and Biomedical Investigations (MIBBI) checklists (Taylor et al. 2008
). The software is open source and adheres to the promotion of open source file formats, such as mzML and nmrML. MetaboLights will ultimately consist of a reference later on top of the repository layer. The reference layer will contain information about individual metabolites and their chemical, analytical and biological properties. The repository later, which has been launched and is fully operational, contains primary research data from published metabolomics studies, annotated with meta data (Fig. ). One of the main submission channels for MetaboLights is the ISA Tools Suite (Fig. ) (Sansone et al. 2012
MetaboLights general outline with repository and reference layer. The reference layer is work currently in progress
MetaboLights data submission workflow
MetaboLights is not intended 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, Metabolic Profiling Forum (Metabomeeting) and the Metabolomics Standards Initiative (MSI). MetaboLights aims at formal data sharing agreements with major resources such as the Human Metabolome Database, the Golm Metabolome Database and the Rikken Metabolomics Platform. Currently we house a selection of experimental raw data and their associated metadata for different platforms such as NMR, GC-MS and LC-MS (Fig. ). The repository layer is generally open to any data that was used in a metabolomics study. That could include, for instance, flux data (temporal measurements with 13C), spatial maps, and IR and Raman fingerprint data.
MetaboLights search results
Call for submitting data
MetaboLights is now ready for receiving metabolomics datasets. We have, for example, recently received the validation dataset measured by O’Callaghan et al
. for validating their PyMS software (O’Callaghan et al. 2012
). We think that this is the way forward for sharing gold standard datasets for validating metabolomics software. Generally, we hope, and will work towards this with journal editors, that the submission of datasets used to justify findings in publications will be submitted to the MetaboLights or one of the emerging collaborating repositories. Interested readers are encouraged to go to http://www.ebi.ac.uk/metabolights/presubmit
and submit their data. The MetaboLights team is happy to assist in this process.