The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations]
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 ELIX...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2017-10-01
|
| Series: | F1000Research |
| Subjects: | |
| Online Access: | https://f1000research.com/articles/6-1649/v2 |
| _version_ | 1818277089858551808 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Merlijn van Rijswijk |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T22:56:00Z |
| format | Article |
| id | doaj.art-c94085c689b54380a553c8703294e419 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-12T22:56:00Z |
| publishDate | 2017-10-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-c94085c689b54380a553c8703294e4192022-12-22T00:08:56ZengF1000 Research LtdF1000Research2046-14022017-10-01610.12688/f1000research.12342.213993The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations]Merlijn van Rijswijk0Charlie Beirnaert1Christophe Caron2Marta Cascante3Victoria Dominguez4Warwick B. Dunn5Timothy M. D. Ebbels6Franck Giacomoni7Alejandra Gonzalez-Beltran8Thomas Hankemeier9Kenneth Haug10Jose L. Izquierdo-Garcia11Rafael C. Jimenez12Fabien Jourdan13Namrata Kale14Maria I. Klapa15Oliver Kohlbacher16Kairi Koort17Kim Kultima18Gildas Le Corguillé19Pablo Moreno20Nicholas K. Moschonas21Steffen Neumann22Claire O’Donovan23Martin Reczko24Philippe Rocca-Serra25Antonio Rosato26Reza M. Salek27Susanna-Assunta Sansone28Venkata Satagopam29Daniel Schober30Ruth Shimmo31Rachel A. Spicer32Ola Spjuth33Etienne A. Thévenot34Mark R. Viant35Ralf J. M. Weber36Egon L. Willighagen37Gianluigi Zanetti38Christoph Steinbeck39ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, NetherlandsADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, BelgiumELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, FranceDepartment of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, SpainELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, FranceSchool of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UKComputational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UKINRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, FranceOxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UKNetherlands Metabolomics Center, Leiden, 2333 CC, NetherlandsEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKCentro Nacional Investigaciones Cardiovasculares, Madrid, 28029, SpainELIXIR Hub, Cambridge, CB10 1SD, UKToxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, FranceEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKMetabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology – Hellas (FORTH/ICE-HT), Patras, GR-26504, GreeceBiomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, GermanyThe Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, EstoniaDepartment of Medical Sciences, Uppsala University, Uppsala, 752 36, SwedenUPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, FranceEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKDepartment of General Biology, School of Medicine, University of Patras, Patras, GR-26504, GreeceDepartment of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, GermanyEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKBSRC “Alexander Fleming”, Athens, GR-16672, GreeceOxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UKMagnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, ItalyEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKOxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UKLuxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, LuxembourgDepartment of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, GermanyThe Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, EstoniaEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UKDepartment of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, SwedenCEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, FranceSchool of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UKSchool of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UKDepartment of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, NetherlandsCRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, ItalyFriedrich-Schiller-University, Jena, 07743, GermanyMetabolomics, 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.https://f1000research.com/articles/6-1649/v2Chemical Biology of the Cell |
| spellingShingle | 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 The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] F1000Research Chemical Biology of the Cell |
| title | The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] |
| title_full | The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] |
| title_fullStr | The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] |
| title_short | The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations] |
| title_sort | future of metabolomics in elixir version 2 referees 2 approved 1 approved with reservations |
| topic | Chemical Biology of the Cell |
| url | https://f1000research.com/articles/6-1649/v2 |
| work_keys_str_mv | AT merlijnvanrijswijk thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT charliebeirnaert thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT christophecaron thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT martacascante thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT victoriadominguez thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT warwickbdunn thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT timothymdebbels thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT franckgiacomoni thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT alejandragonzalezbeltran thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT thomashankemeier thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kennethhaug thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT joselizquierdogarcia thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rafaelcjimenez thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT fabienjourdan thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT namratakale thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT mariaiklapa thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT oliverkohlbacher thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kairikoort thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kimkultima thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT gildaslecorguille thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT pablomoreno thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT nicholaskmoschonas thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT steffenneumann thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT claireodonovan thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT martinreczko thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT philipperoccaserra thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT antoniorosato thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rezamsalek thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT susannaassuntasansone thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT venkatasatagopam thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT danielschober thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT ruthshimmo thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rachelaspicer thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT olaspjuth thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT etienneathevenot thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT markrviant thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT ralfjmweber thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT egonlwillighagen thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT gianluigizanetti thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT christophsteinbeck thefutureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT merlijnvanrijswijk futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT charliebeirnaert futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT christophecaron futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT martacascante futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT victoriadominguez futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT warwickbdunn futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT timothymdebbels futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT franckgiacomoni futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT alejandragonzalezbeltran futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT thomashankemeier futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kennethhaug futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT joselizquierdogarcia futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rafaelcjimenez futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT fabienjourdan futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT namratakale futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT mariaiklapa futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT oliverkohlbacher futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kairikoort futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT kimkultima futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT gildaslecorguille futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT pablomoreno futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT nicholaskmoschonas futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT steffenneumann futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT claireodonovan futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT martinreczko futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT philipperoccaserra futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT antoniorosato futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rezamsalek futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT susannaassuntasansone futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT venkatasatagopam futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT danielschober futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT ruthshimmo futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT rachelaspicer futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT olaspjuth futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT etienneathevenot futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT markrviant futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT ralfjmweber futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT egonlwillighagen futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT gianluigizanetti futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations AT christophsteinbeck futureofmetabolomicsinelixirversion2referees2approved1approvedwithreservations |