MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

By Kenneth Haug, R. Salek, Pablo Conesa, Janna Hastings, P. Matos, M. Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, P. Rocca-Serra and 5 more. Nucleic Acids Res., 2012

623 citations recorded by the source corpus.

MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.

Subfields: Complementary and alternative medicine, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/28dd9bd4ded2353f1cfef1ded67d1a207ee3474d

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In Complementary and alternative medicine

Oliver Fiehn

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Citations in the corpus

NOREVA: normalization and evaluation of MS-based metabolomics data (2017, methodology): “Detailed information of these five datasets were also provided on the web-site of the MetaboLights (55) and in the related publications (28,33).”
Predicting Network Activity from High Throughput Metabolomics (2013, methodology): “Analysis of human urine and yeast data Data on human urinary samples [63] were retrieved from MetaboLights server [71].”
MetaboLights: a resource evolving in response to the needs of its scientific community (2019, background): “We describe the significant developments that we have made with a focus on how we are positioning MetaboLights (1) to address its increasing use in biosciences.”
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research (2017, background): “This work was triggered by the coming of age of the metabolomics field (16), resulting in a growing amount of experimental data (17).”
ArrayExpress update – from bulk to single-cell expression data (2018, background): “It is also now possible to add links leading to related ArrayExpress experiments, or related data in other EMBL-EBI resources, such as PRIDE (9), ENA (10) and MetaboLights (11).”
Updates in Rhea – an expert curated resource of biochemical reactions (2016, methodology): “Knowledgebases that use Rhea for the annotation of enzyme and metabolite data include the SwissLipids knowledgebase for lipid biology (7), the EBI Enzyme portal (8), the MetaboLights repository of metabolomics data (9) and IntEnz (5).”
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “In fact, very few reports in published research have more than 20% identiﬁed compounds in untargeted analysis, as can be seen at the Metabolomics Workbench [30], or the European metabolomics repository MetaboLights [31].”
The Ontology for Biomedical Investigations (2016, background): “This includes (i) international public repositories such as Metabolights [32] backing deposition of Metabolomics datasets, (ii) research consortia repositories (e.g. ToxBank [33], diXa (http:// www.dixa-fp7.eu), ( iii) standard development groups (e.g. ISA-Tab-Nano [34], COordination of Standards in”
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools (2015, background): “We are currently collaborating with the MetaboLights project team at the European Bioinformatics Institute (EBI) to explore and implement ways to facilitate metabolomics data exchange among different data repositories.”
Review on natural products databases: where to find data in 2020 (2020, methodology): “The database is not available yet, but the data has been already published in the MetaboLights [87] repository for metabolomics experimental data.”
The role of reporting standards for metabolite annotation and identification in metabolomic studies (2013, background): “MetaboLights is the first general purpose database in metabolomics and became operational in 2012 [5].”