F1000Research (Oct 2017)
The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations]
- Merlijn van Rijswijk,
- Charlie Beirnaert,
- Christophe Caron,
- Marta Cascante,
- Victoria Dominguez,
- Warwick B. Dunn,
- Timothy M. D. Ebbels,
- Franck Giacomoni,
- Alejandra Gonzalez-Beltran,
- Thomas Hankemeier,
- Kenneth Haug,
- Jose L. Izquierdo-Garcia,
- Rafael C. Jimenez,
- Fabien Jourdan,
- Namrata Kale,
- Maria I. Klapa,
- Oliver Kohlbacher,
- Kairi Koort,
- Kim Kultima,
- Gildas Le Corguillé,
- Pablo Moreno,
- Nicholas K. Moschonas,
- Steffen Neumann,
- Claire O’Donovan,
- Martin Reczko,
- Philippe Rocca-Serra,
- Antonio Rosato,
- Reza M. Salek,
- Susanna-Assunta Sansone,
- Venkata Satagopam,
- Daniel Schober,
- Ruth Shimmo,
- Rachel A. Spicer,
- Ola Spjuth,
- Etienne A. Thévenot,
- Mark R. Viant,
- Ralf J. M. Weber,
- Egon L. Willighagen,
- Gianluigi Zanetti,
- Christoph Steinbeck
Affiliations
- Merlijn van Rijswijk
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands
- Charlie Beirnaert
- ADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
- Christophe Caron
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
- Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain
- Victoria Dominguez
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
- Warwick B. Dunn
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
- Timothy M. D. Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
- Franck Giacomoni
- INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, France
- Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
- Thomas Hankemeier
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
- Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Jose L. Izquierdo-Garcia
- Centro Nacional Investigaciones Cardiovasculares, Madrid, 28029, Spain
- Rafael C. Jimenez
- ELIXIR Hub, Cambridge, CB10 1SD, UK
- Fabien Jourdan
- Toxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, France
- Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Maria I. Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology – Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece
- Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
- Kairi Koort
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia
- Kim Kultima
- Department of Medical Sciences, Uppsala University, Uppsala, 752 36, Sweden
- Gildas Le Corguillé
- UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, France
- Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Nicholas K. Moschonas
- Department of General Biology, School of Medicine, University of Patras, Patras, GR-26504, Greece
- Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
- Claire O’Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Martin Reczko
- BSRC “Alexander Fleming”, Athens, GR-16672, Greece
- Philippe Rocca-Serra
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
- Antonio Rosato
- Magnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, Italy
- Reza M. Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Susanna-Assunta Sansone
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
- Venkata Satagopam
- Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
- Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
- Ruth Shimmo
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia
- Rachel A. Spicer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
- Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, Sweden
- Etienne A. Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, France
- Mark R. Viant
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
- Ralf J. M. Weber
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
- Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, Netherlands
- Gianluigi Zanetti
- CRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, Italy
- Christoph Steinbeck
- Friedrich-Schiller-University, Jena, 07743, Germany
- DOI
- https://doi.org/10.12688/f1000research.12342.2
- Journal volume & issue
-
Vol. 6
Abstract
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
Keywords
