MetaboLights

Resource for Metabolomics/Lipidomics experiments and derived information

Description

Database for Metabolomics/Lipidomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals and Elixir. We collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Technical Information

Website:
https://www.ebi.ac.uk/metabolights/

Covered lipid categories:
FA;GL;GP;SP;ST;PR;SL;PK;

Publications:
PMID: 37971328

Documentation:
https://ebi-metabolights.github.io/guides/

Download / Web-service:
Download metadata files using MetaboLights Editor or API. To download data files, MetaboLights Editor, FTP, Aspera or Globus clients. https://www.ebi.ac.uk/metabolights/download

API:
https://www.ebi.ac.uk/metabolights/ws3/api

Source code:
https://github.com/EBI-Metabolights

Programming languages:
Java, Python, Javascript

Platforms:
Kubernetes

Input formats:
Txt, .tsv, raw and derived files formats

Output formats:
Txt, .tsv, JSON, raw and derived files formats

Interface:
Web platform, GUI, CLI

Licence:
Creative Commons Public Domain (CC0) License for MetaboLights datasets submitted from April 2025 (https://creativecommons.org/public-domain/cc0) and EBI terms of use (https://www.ebi.ac.uk/about/terms-of-use) for datasets submitted before April 2025.

Sections

Section 2 — Lipidomics Data Repository

Analysis types:
MS (LC-MS, GC-MS, DI-MS, MS-Imaging, FIA-MS, CE-MS, GCxGC-MS), NMR, LC-DAD, GC-FID

Number of datasets:
2,389

Dataset curation:
https://www.ebi.ac.uk/metabolights/editor/console

Experimental metadata:
Yes (Required for study submission and available to download): Metadata is structured using the Investigation, Study, and Assay (ISA)-Tab file format and linked to community-developed controlled vocabularies and ontologies whenever possible

Raw data:
Yes (Required for study submission and available to download). Raw file formats: baf, cmp, d, dat, fid, hr, ibd, jpf, lcd, ms, peg, qgd, raw, ser, wiff + wiff.scan, smp

Processed data:
Yes (List of identified lipids/metabolites; relative and absolute quantities; available for download). Derived file formats: cdf, cef^, cnx^, dx^, imzml, mgf^, msp^, mzml, mzxml, nmrml, peakml^, xlsx^, xy^ (^ not acceptable alone - must be accompanied with spectrum / chromatogram data).