COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
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.
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.
Reza M
RM
Salek
Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany.
Steffen
S
Neumann
Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany.
Daniel
D
Schober
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Jan
J
Hummel
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Kenny
K
Billiau
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Joachim
J
Kopka
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess St., Manchester, M1 7DN UK.
Elon
E
Correa
Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
Theo
T
Reijmers
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy.
Antonio
A
Rosato
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy ; FiorGen Foundation, 50019 Sesto Fiorentino, FI Italy.
Leonardo
L
Tenori
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy.
Paola
P
Turano
Department of Biochemistry and Molecular Biology, Faculty of Biology, IBUB, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain.
Silvia
S
Marin
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.
Catherine
C
Deborde
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.
Daniel
D
Jacob
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.
Dominique
D
Rolin
Centre of bioinformatics of Bordeaux (CBiB), University of Bordeaux, 33000 Bordeaux, France.
Benjamin
B
Dartigues
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
Pablo
P
Conesa
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
Kenneth
K
Haug
University of Oxford e-Research Centre, 7 Keble Road, Oxford, OX1 3QG UK.
Philippe
P
Rocca-Serra
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess St., Manchester, M1 7DN UK.
Steve
S
O'Hagan
Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London, SW7 2AZ UK.
Jie
J
Hao
Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
Michael
M
van Vliet
Zora Biosciences OY, 02150 Espoo, Finland.
Marko
M
Sysi-Aho
School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.
Christian
C
Ludwig
Microbiology & Systems Biology, TNO, Zeist, The Netherlands.
Jildau
J
Bouwman
Department of Biochemistry and Molecular Biology, Faculty of Biology, IBUB, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain.
Marta
M
Cascante
Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London, SW7 2AZ UK.
Timothy
T
Ebbels
Medical Research Council Human Nutrition Research, Fulbour Road, Cambridge, CB1 9NL UK ; Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK.
Julian L
JL
Griffin
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.
Annick
A
Moing
University of Bordeaux, CBiB/LaBRI, 33000 Bordeaux, France.
Macha
M
Nikolski
Zora Biosciences OY, 02150 Espoo, Finland.
Matej
M
Oresic
University of Oxford e-Research Centre, 7 Keble Road, Oxford, OX1 3QG UK.
Susanna-Assunta
SA
Sansone
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.
Mark R
MR
Viant
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess St., Manchester, M1 7DN UK.
Royston
R
Goodacre
School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.
Ulrich L
UL
Günther
Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
Thomas
T
Hankemeier
Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI Italy.
Claudio
C
Luchinat
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Dirk
D
Walther
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
Christoph
C
Steinbeck
Coordination and data sharing community; Data exchange; Data standards; Metabolomics; Metabonomics; e-Infrastructure