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Following the success of global efforts to exchange genomic and other biomedical data, we have now witnessed the emergence of global databases in metabolomics. The MetaboLights database, the first general purpose, cross-species, cross-application database in metabolomics, became the fastest growing data repository at the EMBL-EBI in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights through user submissions. User submission of data to public repositories such as MetaboLights are now not only encouraged by publishers and funders but can now also directly benefit the publication record of a scientist by describing the published dataset in a data publication in journals such as Nature Scientific Data.