COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access Reza Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo Reijmers, Antonio Rosato, Leonardo Tenori, et al. To cite this version: Reza Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, et al.. COordina- tion of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics, Springer Verlag, 2015, 11 (6), pp.Journal no. 11306. 10.1007/s11306-015-0810-y. hal-01165673 HAL Id: hal-01165673 https://hal.archives-ouvertes.fr/hal-01165673 Submitted on 27 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Metabolomics DOI 10.1007/s11306-015-0810-y ORIGINAL ARTICLE COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access 1,15 2 2 3 Reza M. Salek • Steffen Neumann • Daniel Schober • Jan Hummel • 3 3 10 12 Kenny Billiau • Joachim Kopka • Elon Correa • Theo Reijmers • 4 4,19 4 5 Antonio Rosato • Leonardo Tenori • Paola Turano • Silvia Marin • 6 6 6 7 Catherine Deborde • Daniel Jacob • Dominique Rolin • Benjamin Dartigues • 1 1 8 10 Pablo Conesa • Kenneth Haug • Philippe Rocca-Serra • Steve O’Hagan • 16 12 13 17 Jie Hao • Michael van Vliet • Marko Sysi-Aho • Christian Ludwig • 11 5 16 14,15 Jildau Bouwman • Marta Cascante • Timothy Ebbels • Julian L. Griffin • 6 9 13 8 Annick Moing • Macha Nikolski • Matej Oresic • Susanna-Assunta Sansone • 18 10 17 12 Mark R. Viant • Royston Goodacre • Ulrich L. Gu¨nther • Thomas Hankemeier • 4 3 1 Claudio Luchinat • Dirk Walther • Christoph Steinbeck Received: 26 September 2014 / Accepted: 14 May 2015 Ó The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Metabolomics has become a crucial phenotyp- publishers and funders. After the initial efforts of the meta- ing technique in a range of research fields including medi- bolomics standards initiative, minimum reporting standards cine, the life sciences, biotechnology and the environmental were proposed which included the concepts for metabo- sciences. This necessitates the transfer of experimental in- lomics databases. Built by the community, standards and formation between research groups, as well as potentially to infrastructure for metabolomics are still needed to allow & Christoph Steinbeck 9 University of Bordeaux, CBiB/LaBRI, 33000 Bordeaux, [email protected] France 10 School of Chemistry & Manchester Institute of 1 European Molecular Biology Laboratory, European Biotechnology, University of Manchester, 131 Princess St., Bioinformatics Institute (EMBL-EBI), Wellcome Trust Manchester M1 7DN, UK Genome Campus, Hinxton, Cambridge CB10 1SD, UK 11 Microbiology & Systems Biology, TNO, Zeist, 2 Department of Stress and Developmental Biology, Leibniz The Netherlands Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany 12 Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, 3 Max Planck Institute of Molecular Plant Physiology, The Netherlands 14476 Potsdam-Golm, Germany 13 Zora Biosciences OY, 02150 Espoo, Finland 4 Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, FI, Italy 14 Medical Research Council Human Nutrition Research, Fulbour Road, Cambridge CB1 9NL, UK 5 Department of Biochemistry and Molecular Biology, Faculty of Biology, IBUB, Universitat de Barcelona, Diagonal 643, 15 Department of Biochemistry, University of Cambridge, 08028 Barcelona, Spain Cambridge CB2 1GA, UK 6 INRA, Univ. Bordeaux, UMR1332 Fruit Biology and 16 Computational and Systems Medicine, Department of Pathology, Metabolome Facility of Bordeaux - MetaboHUB, Surgery and Cancer, Imperial College London, South Functional Genomics Center, IBVM, Centre INRA Kensington, London SW7 2AZ, UK Bordeaux, 71 av Edouard Bourlaux, 17 School of Cancer Sciences, University of Birmingham, 33140 Villenave d’Ornon, France Edgbaston, Birmingham B15 2TT, UK 7 Centre of bioinformatics of Bordeaux (CBiB), University of 18 School of Biosciences, University of Birmingham, Bordeaux, 33000 Bordeaux, France Edgbaston, Birmingham B15 2TT, UK 8 University of Oxford e-Research Centre, 7 Keble Road, 19 FiorGen Foundation, 50019 Sesto Fiorentino, FI, Italy Oxford OX1 3QG, UK 123 R. M. Salek et al. storage, exchange, comparison and re-utilization of meta- industrial and domestic chemicals but also for the safety bolomics data. The Framework Programme 7 EU Initiative assessments of engineered nanomaterials as well as novel ‘coordination of standards in metabolomics’ (COSMOS) is compounds generated through synthetic biology. developing a robust data infrastructure and exchange stan- Considering the diversity and breadth of metabolomics dards for metabolomics data and metadata. This is to support applications, not forgetting complexity and diversity of the workflows for a broad range of metabolomics applications analytical technologies in use, there is a clearly identified within the European metabolomics community and the need for standardisation that evolves with the technologies wider metabolomics and biomedical communities’ par- and is sufficiently inclusive to cover all metabolomics ticipation. Here we announce our concepts and efforts asking applications. for re-engagement of the metabolomics community, aca- demics and industry, journal publishers, software and hardware vendors, as well as those interested in stan- 2 What has been achieved so far in metabolomics dardisation worldwide (addressing missing metabolomics standards ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards The momentum for metabolomics standards started in updating and implementing metabolomics standards. 2004–2005 with initiatives such as the standard metabolic reporting structure initiative or SMRS (Lindon et al. 2005) Keywords Metabolomics Á Metabonomics Á Data and the Architecture for Metabolomics consortium or standards Á Data exchange Á e-Infrastructure Á Coordination Armet (Jenkins et al. 2004); these were mainly focused on and data sharing community an aspect of metabolomics standards, for example nuclear magnetic resonance (NMR) based metabonomics or plant- based metabolomics. There were several other initiatives at 1 Introduction the time, however all efforts eventually resulted in the formation of the metabolomics standards initiative (MSI) Metabolomics (Bundy et al. 2009; Clayton et al. 2006; in 2005 (Castle et al. 2006; Fiehn et al. 2006). This was Eckhart et al. 2012; Holmes et al. 2008)1 and fluxomics focused on community-agreed minimum reporting stan- (metabolic flux analysis, Zamboni, Nicola et al. ‘‘13C-based dards and providing initial efforts on the descriptions of the metabolic flux analysis.’’ Nature protocols 4.6 (2009): experimental metadata describing a metabolomics study. 878–892) measurements mark the end point closest to the This culminated in a series of manuscripts published in phenotype of organisms, reflecting changes in organisms 2007 that considered all the components undertaken in influenced by external parameters such as nutritional, envi- metabolomics experiments (Sansone et al. 2007; Fiehn ronmental or toxicological interactions. In this context, due et al. 2007; Hardy and Taylor 2007) summarized in to its dynamic nature, metabolomics is of considerable value (Goodacre 2014). One major outcome was the formation of for examples in personalised medicine, especially as it five different working groups (WG) to consider each aspect captures rapid responses close to the phenotype and in of the metabolomic pipeline; biological context metadata concert with the genome, transcriptome and epigenome (van WG, chemical analysis WG, data processing WG, ontology der Greef et al. 2006, Nicholson et al. 2011). For such WG and exchange format WG, with the task of collecting methods to succeed in a personalised medicine context, ro- relevant metabolomics standards and a forum for discus- bust traceable standardisation is essential, covering storage sion (Goodacre et al. 2007; Morrison et al. 2007; Rubtsov and exchange of metabolomics and fluxomics data. More- et al. 2007; Sumner et al. 2007; Werf et al. 2007). How- over, new applications that link metabolomics and biobanks ever, there have been limited practical applications for such are emerging: metabolomics may be used as an efficient tool descriptions, with some exceptions (Ludwig et al. 2012; to monitor the quality of stored samples and to establish the Bais et al. 2010; Ferry-Dumazet et al. 2011; Griffin et al. optimal standard operating procedures (SOPs) for the pre- 2011; Scholz and Fiehn 2007), in part owing to a lack of analytical handling of bio-specimens (Bernini et al. 2011). tools to facilitate implementation or a widely used database Metabolomics is rapidly becoming an essential tool in the to enforce such standards. Most projects or databases fo- screening of food products, which is highly regulated and cused on one particular technology