MAP/UK Partner site: The europian bioinformatics institute (EMBL-EBI)

The Metabolomics team at EMBL-EBI

Metabolomics is the study of small molecule metabolites in the metabolome, which is the complete set of metabolites in a biological sample. It allows us to detect disease states and their progression, monitor responses to therapy, stratify patients based on biochemical profiles, and highlight targets for drug design. We maintain MetaboLights, a global public resource for data from 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. Our main focus is on expanding the coverage and depth of metabolomics data available to the community.

Critical to achieving this is the development of our submission procedures to address our diverse user community. We provide an online editor which guides the submitter through the process, with constant validation and context specific data requirements and ontologies. For more large scale depositors such as the phenome centres (eg Birmingham University) and commercial companies (eg Metabolon), we provide an API to allow template submissions at scale. To also improve the depth of the data, we continue the development of MetaboLights Labs, a workbench providing the infrastructure for metabolomics data processing and analysis and submission to MetaboLights and have developed a course Introduction to Metabolomics Analysis (delivered to an international group of students at EMBL-EBI) to provide guidance on the metabolomics field and to ensure data quality. Related to this is the delivery of PhenoMeNal which is part of the course and integrated with MetaboLights Labs to ensure consistent, reproducible and audited workflows. We became an ELIXIR recommended repository and established the ELIXIR Metabolomics Community and have been successful in being awarded an Implementation study for Metabolite identification.

We have been an active member in multiple standardisation efforts in untargeted metabolomics including the establishment of the Metabolomics Quality Assurance and Quality Control Consortium (mQACC), the OECD Metabolomics and Metabolomics GO FAIR Implementation Networks.We also expanded our impact across the global research community, establishing closer interactions with our US collaborator Metabolomics Workbench through the NIH Commons Metabolomics Program stage II and with our Japanese colleagues at the National Insitute of Genetics which hosts Metabolonote.