The Metabolomics Standards Initiative (MSI)

Original working group chairs

What is New?

COSMOS (COordination Of Standards In MetabOlomicS) -  a global effort to enable free and open sharing of metabolomics data. Coordinated by EMBL-European Bioinformatics Institute, COSMOS (Coordination of Standards in Metabolomics) has brought together European metabolomics data providers to set and promote community standards.

Data standards: The COSMOS work on standardisation was built on the foundational work by PSI and MSI and further develop and contribute to data exchange formats, ranging from raw data in MS and NMR, the reporting of metabolite quantification and metabolite identification, to the experimental metadata. COSMOS has extended the open standards for MS data exchange initiated by PSI, such as mzML and mzQuantML to meet the requirement of metabolomics standards for reporting MS experiments.

COSMOS has also developed the missing open standard, the NMR Markup Language (nmrML) for capturing and disseminating Nuclear Magnetic Resonance spectroscopy raw data in metabolomics, including data converter web services to ease nmrML generation from proprietary vendor has formats. In addition COSMOS implemented a semantic validation set-up to check nmrML raw data on plausibility and completeness, contributing to open access processing quality assurance and robust long term storage, more details at (http://nmrml.org/). The first dataset with the nmrML data format can be found at MetaboLights- MTBLS1. 

Linking with e-infrastructures: In addition to capturing and storing extremely large volumes of data, e-infrastructures must be capable of disseminating these data based on open and widely accepted community standards. Such initiatives were well timed, as it coincided with the development of repositories such as MetaboLights (www.ebi.ac.uk/metabolights) and the growing support for life science e-infrastructures such as ELIXIR, EU-OPENSCREEN and BBMRI and NIH funded Metabolomics Works Bench.

MetabolomeXchange: To foster distribution of experimental metabolomics data among the research community, COSMOS has setup RSS based solutions to federate data available from the leading metabolomics data repositories (MetaboLights, Metabolomic Repository Bordeaux, Max Planck Institute - MPIMP and Metabolomics Workbench). To this end, we have initiated the MetabolomeXchange consortium, currently comprised of four metabolomics data providers. The www.metabolomeXchange.org web site, was officially launched in June 1st 2014,  during the Metabolomics 2014 conference in Japan later that month. In the months after several improvements were made and on September 1st 2015 MX released a completely new version. MX facilitates access and linkage to publically available datasets and is updated automatically every hour, contributing to dissemination of metabolomics data globally.

​​History: The Metabolomics Standards Initiative (MSI) was conceived in 2005, as an initiative of Metabolomics Society activities, now coordinated by the Data Standards Task Group of the Society. The MSI is an academic policy provider, to support the development of open data and metadata formats for metabolomics. MSI followed on earlier work by the Standard Metabolic Reporting Structure initiative (report) and the Architecture for Metabolomics consortium (ArMet). The early efforts of MSI were focused on community-agreed reporting standards, the so called minimal information (MI) checklists and data exchange formats to support the MIs reporting standards. MSI aims was to provide a clear description of the biological system studied and all components of a metabolomics study as well as to allow data to be efficiently applied, shared and reused. Out of 2004-2007 society meetings and discussions five working groups were established. For example, the chemical analysis group proposed minimum information for reporting chemical analysis, including minimum metadata reporting related to metabolite identification. Therefore, several cross-communicating working groups were built to cover the development of different aspects of metabolomics experiment data standardisation

Working Groups: The following MSI WGs were created to reflect on different areas in metabolomics  standards.

1. Core Information for Metabolomics Reporting (CIMR): This document specified the minimal guidelines for reporting metabolomics experiments. The minimum information (MI) was captured in a textual form, aiming to cover all application areas and analysis technologies. This document was developed by the biological context metadata WG, the chemical analysis WG, the data processing WG, the exchange format WG and the ontology WG.
2. Ontology: The CV and ontology was developed iteratively by the ontology WG on the basis of CIMR. This work was carried out in collaboration with: HUPO-PSI, FGED (MGED) and OBI ontology (former FuGO).
   
3. Exchange format: A data model and exchange format was developed by the exchange format WG on the basis of CIMR, making use of the MSI ontology. This work was also in collaboration with the HUPO-PSI and FUGE initiatives.
4. ​Biological context metadata WG
   
   • In-vivo / mammalian biology context
     
   • Plant biology context
     
   • In vitro biology/microbiology context
     
   • Environmental analysis context