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Metabolomics. 2015;11(6):1587-1597. Epub 2015 May 26.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK ; Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK.
2
Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany.
3
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
4
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess St., Manchester, M1 7DN UK.
5
Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
6
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy.
7
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy ; FiorGen Foundation, 50019 Sesto Fiorentino, FI Italy.
8
Department of Biochemistry and Molecular Biology, Faculty of Biology, IBUB, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain.
9
INRA, Univ. Bordeaux, UMR1332 Fruit Biology and Pathology, Metabolome Facility of Bordeaux - MetaboHUB, Functional Genomics Center, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France.
10
Centre of bioinformatics of Bordeaux (CBiB), University of Bordeaux, 33000 Bordeaux, France.
11
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
12
University of Oxford e-Research Centre, 7 Keble Road, Oxford, OX1 3QG UK.
13
Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London, SW7 2AZ UK.
14
Zora Biosciences OY, 02150 Espoo, Finland.
15
School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.
16
Microbiology & Systems Biology, TNO, Zeist, The Netherlands.
17
Medical Research Council Human Nutrition Research, Fulbour Road, Cambridge, CB1 9NL UK ; Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK.
18
University of Bordeaux, CBiB/LaBRI, 33000 Bordeaux, France.
19
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.

Abstract

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

KEYWORDS:

Coordination and data sharing community; Data exchange; Data standards; Metabolomics; Metabonomics; e-Infrastructure

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