MetaboLights: An Open‐Access Database Repository for Metabolomics Data

Abstract

MetaboLights is the first general purpose, open‐access database repository for cross‐platform and cross‐species metabolomics research at the European Bioinformatics Institute (EMBL‐EBI). Based upon the open‐source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user‐friendly submission tools. © 2016 by John Wiley & Sons, Inc.

Recent Advances in NMR-Based Metabolomics

“…Another international open-access database repository, MetaboLights, collects data from cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). 170 It provides Metabolomics Standard Initiative compliant metadata and raw experimental data associated with metabolomics experiments. These data repositories and new software tools are already being heavily used and promise to have a large impact on the field.…”

Enzyme annotation in UniProtKB using Rhea

“…Here we describe the introduction of Rhea as the reference vocabulary for enzyme annotation in UniProtKB. This development will significantly increase the utility of UniProtKB for applications such as the integrative analysis of metabolomics and other 'omics data (Kale, et al, 2016;Sud, et al, 2016), as illustrated here, as well as the study of enzyme chemistry and evolution (Rahman, et al, 2016;Tyzack, et al, 2019), the construction and annotation of metabolic models (Cottret, et al, 2018;King, et al, 2016;Moretti, et al, 2016), and the engineering of pathways for biosynthesis and bioremediation (Duigou, et al, 2019). Rhea will also provide a basis to further improve links with other knowledge resources, such as the Gene Ontology (The Gene Ontology Consortium, 2019) and Reactome (Fabregat, et al, 2018), which both plan to use Rhea as the reference for reaction chemistry (Chris Mungall and Peter D'Eustachio, personal communication).…”

“…We also plan to extend the use of ChEBI within UniProtKB to describe all small molecule chemical structure data, including functionally important ligands and post-translational modifications (see https://www.uniprot.org/docs/ptmlist). This will further improve links and interoperability between UniProtKB and other resources that use ChEBI such as the metabolomics data repository MetaboLights (Kale, et al, 2016), the IMEx molecular interaction databases (Orchard, et al, 2012) and the Complex Portal (Meldal, et al, 2015), the literature annotation services of Europe PubMed Central (Europe PMC Consortium, 2015), the BioModels repository (Glont, et al, 2018), and the Immune Epitope Database (IEDB) (Dhanda, et al, 2019).…”

Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems

“…The idea behind crowd-sourcing is to have thousands of individual laboratories or investigators randomly collect and deposit spectra of purified compounds into common, open-access repositories. This is the basis to databases such as GNPS, MetaboLights and MassBank of North America (MoNA) [116,147,149]. Certainly, if scientific journals and publishing houses were to buy into this crowd-sourcing concept then the cost of such an effort could be greatly reduced and the time to complete the process could be significantly shortened.…”