D440–D444 Nucleic Acids Research, 2020, Vol. 48, Database issue Published online 6 November 2019 doi: 10.1093/nar/gkz1019 MetaboLights: a resource evolving in response to the needs of its scientific community Kenneth Haug , Keeva Cochrane, Venkata Chandrasekhar Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan and Claire O’Donovan *
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Received September 24, 2019; Revised October 17, 2019; Editorial Decision October 17, 2019; Accepted October 31, 2019
ABSTRACT and environmental factors. Metabolomics is a powerful ap- proach because metabolites and their concentrations, un- MetaboLights is a database for metabolomics stud- like other ‘omics measures, directly reflect the underlying ies, their raw experimental data and associated biochemical activity and state of cells / tissues. Because metadata. The database is cross-species and cross- of this, metabolomics best represents the molecular pheno- technique and it covers metabolite structures and type. Metabolomics technologies yield many insights into their reference spectra as well as their biological basic biological research in areas such as systems biology roles and locations. MetaboLights is the recom- and metabolic modelling, pharmaceutical research, nutri- mended metabolomics repository for a number of tion and toxicology. leading journals and ELIXIR, the European infras- Our challenge is to capture the growing amount, depth tructure for life science information. In this article, we and diversity of metabolomic information and to make it describe the significant updates that we have made easily available and interpretable to our users and integrated with the wider ‘omics community. We describe the signifi- over the last two years to the resource to respond cant developments that we have made with a focus on how to the increasing amount and diversity of data being we are positioning MetaboLights (1) to address its increas- submitted by the metabolomics community. We re- ing use in biosciences. freshed the website and most importantly, our sub- mission process was completely overhauled to en- able us to deliver a far more user-friendly submis- PROGRESS AND DEVELOPMENTS sion process and to facilitate the growing demand Growth of submissions for reproducibility and integration with other ‘omics. Metabolomics resources and data are available un- The MetaboLights repository has continued to see con- der the EMBL-EBI’s Terms of Use via the web at https: sistent year on year growth since its first release in 2012, //www.ebi.ac.uk/metabolights and under Apache 2.0 with a particularly notable exponential growth in the last at Github (https://github.com/EBI-Metabolights/). year (Figure 1A). The user base is global with the USA, China and the UK being the top countries for study sub- missions (Figure 1B). At the time of writing, the database INTRODUCTION hosts over 500 publicly available studies with a further 140 Metabolomics is the systematic study of the small molecu- awaiting public release due to publication requirements, and lar metabolites in a cell, tissue, biofluid or cell culture media ∼250 in preparation. MetaboLights supports publications that are the tangible result of cellular processes or responses in a range of journals with a significant proportion not to an environmental stress. Collectively, these metabolites only in specialist metabolomics journals but also in jour- and their interactions within a biological system are known nals from publication groups including Nature, Cell and as the metabolome. Just as genomics is the study of DNA PLOS. The studies in preparation reflect the fact that the and genetic information within a cell, and transcriptomics database is evolving into a resource where data can be de- is the study of RNA and differences in mRNA expres- posited throughout the experimental progress of a study sion; metabolomics is the study of substrates and prod- and in the future, we plan to also provide pre-processing ucts of metabolism, which are influenced by both genetic and analysis capabilities.
*To whom correspondence should be addressed. Tel: +44 1223 494460; Fax: +44 1223 494468; Email: [email protected] Present address: Claire O’Donovan, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinx- ton, Cambridge CB10 1SD, UK.