MetaboLights: a database for metabolomics experiments and derived information

MetaboLights is a database for Metabolomics 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.We will provide search services around spectral similarities and chemical structures.

We offer user-submission tools and have strong reporting capabilities. We will utilise and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole.

MetaboLights semantic quality will be based on various controlled vocabularies linking data to existing resources such as BRENDA (tissue ontology) and other established ontologies. We are dedicated to collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Citing MetaboLights
Kenneth Haug, Reza M. Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendrakar, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire, Alejandra González-Beltrán, Susanna-Assunta Sansone, Julian L. Griffin and Christoph Steinbeck.
MetaboLights-- an open-access general-purpose repository for metabolomics studies and associated meta-data.
Nucl. Acids Res. (2013) doi: 10.1093/nar/gks1004
All data is governed by the EMBL-EBI's Terms of use and all code is licensed under Apache 2.0.


PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications.


MetaboLights submissions are powered by the ISA software suite. so experimental data gets submitted in ISA-Tab format. The Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies.

The MetaboLights project is a member of isacommons, the ISA community.

For submission to MetaboLights, we require submissions to be in the ISA-Tab format. This format can be created and edited using a variety of spreadsheet tools.

We recommend two tools in particular for creation of ISA-Tab files and subsequent submission to our repository:

  • ISAcreator: a standalone desktop application with a multitude of facilities to enable standards-compliant creation of ISA-Tab. More information is available from; and
  • Google Spreadsheets with OntoMaton: OntoMaton is an add-on to Google Spreadsheets enabling ontology search and tagging within the collaborative Google Spreadsheet environment.

A Google Doc template for MetaboLights submissions will be coming soon.

OntoMaton is developed and maintained by the ISA team. You can find out more about OntoMaton from the project page

MetaboLights is the recommended Metabolomics repository for a number of leading journals.

Nature Scientific Data
BioMed Central
PLOS Biology
EMBO press
Wellcome Trust Open Research
F1000 Research
Springer Link - Metabolomics

Through the BioSharing initiative we continue to ensure that a growing number of journals that have data policies endorse MetaboLights as the recommended Metabolomics repository.

BBSCR     EMBL       UC

The development of MetaboLights is funded by the BBSRC, grant reference BB/L024152/1. Previous BBSRC grant reference is BB/I000933/1.
The funding is for a project that will instantiate, at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK, the MetaboLights metabolomics database with various different components focused on both data standards and primary experimental data. MetaboLights is cross-species, cross-application and will cover all relevant analytical methods.

MetaboLights is a joint development between the O’Donovan group at the European Bioinformatics Institute and the Griffin group in Cambridge.