Metabolomics is the study of small molecule metabolites in the metabolome, which is the complete set of metabolites in a biological sample. By studying these metabolites, we can observe changes in cellular networks and biochemical pathways. This could allow us to detect disease states and their progression, monitor responses to therapy, stratify patients based on biochemical profiles, and highlight targets for drug design.

A major bottleneck for this rapidly-expanding field, however, is metabolite identification. Without a comprehensive data set of metabolites to compare against, the results of metabolomics experiments are often hard to interpret.

The goal of the ELIXIR Metabolomics community is to work with experimental scientists and developers to provide the resources, analysis tools and infrastructure that will help metabolite identification. The community will also establish an infrastructure of services, standards and datasets to help researchers discover, annotate and analyse metabolomics data from around Europe.

Goals of the community

The Elixir metabolomics community was created in 2018 and has just started to coordinate its activities. Its goals are:

To create and extend metabolomics datasets

  • Metabolite identification is one of the key problems facing metabolomics researchers. Identification requires high quality curated datasets, and here the reference layer of the MetaboLights database is crucial. The MetaboLights database holds information about individual metabolites, their chemistry, their spectral data (MS, NMR), as well as their role in pathways and biological systems.
  • The compound information in MetaboLights is initially curated in ChEBI, the dictionary of small chemical compounds.
  • The ELIXIR metabolomics community aims to submit missing compound data from metabolomes into ChEBI and therefore enable MetaboLights to connect this data to metabolomes and be more comprehensive. This curated data (spectra, compounds, networks) will also be valuable as input for other reference repositories and e-infrastructures (e.g. MetExplore, Workflow4Metabolomics, PhenoMeNal).
  • The community aims to use this information to create a FAIR data set for identified metabolites comprising various types of mass spectral data with the relevant metadata, and the associated quality of the identification.. This data set will be closely linked to MetaboLights.

To develop data analysis workflows for metabolomics

  • The community will work with workflow management e-infrastructures such as Workflow4Metabolomics, PhenoMeNal, and Galaxy-M to develop the user-friendly, modular, and reproducible data analysis needed by the experimental community.
  • The community will develop comprehensive workflows for preprocessing, statistical analysis and annotation of data from LC-MS, direct infusion MS (DIMS), GC-MS, and NMR technologies. These will be run, saved, shared, and publicly referenced with digital object identifiers and included in the ELIXIR registry.

To promote data standards and interoperability in metabolomics

To support computing with large-scale metabolomics data

  • The PhenoMeNal e-infrastructure enables researchers to deploy and test metabolomics workflows in public clouds (Amazon EC2, Google Cloud Platform) or in-house OpenStack environments in cases where sensitive data cannot leave the institution.
  • The ELIXIR metabolomics community will build on the PhenoMeNal compute infrastructure to provide further workflows for metabolomics that include the identification of metabolites in metabolomics experiments and the mapping onto biological pathways with neighbouring omics areas.

To increase the metabolomics training available

  • There is only one course dedicated to metabolite identification in Europe (at the Birmingham Metabolomics Training Centre). The ELIXIR metabolomics community aims to expand the delivery of metabolomics courses, for example through the European Metabolomics Training Coordination Group network.
  • It will create training partnerships with instrument vendors to increase the quality of training material and facilities.


Christoph Steinbeck
Christoph Steinbeck
(ELIXIR Germany)
Thomas Hankemeier
Thomas Hankemeier
(ELIXIR Netherlands)
Claire O'Donovan
Claire O’Donovan
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Merlijn Van Rijswijk
(ELIXIR Netherlands)
John Hancock
John Hancock
(ELIXIR Services and Communities Coordinator, ELIXIR Hub)

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