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A community proposal to integrate proteomics activities in ELIXIR

JA. Vizcaíno, M. Walzer, RC. Jiménez, W. Bittremieux, D. Bouyssié, C. Carapito, F. Corrales, M. Ferro, AJR. Heck, P. Horvatovich, M. Hubalek, L. Lane, K. Laukens, F. Levander, F. Lisacek, P. Novak, M. Palmblad, D. Piovesan, A. Pühler, V....

. 2017 ; 6 (-) : . [pub] 20170613

Jazyk angličtina Země Anglie, Velká Británie

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc17032053

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

Analytical Biochemistry Department of Pharmacy University of Groningen Groningen 9713 AV Netherlands

Applied Bioinformatics Department of Computer Science University of Tübingen Tübingen 72074 Germany Center for Bioinformatics Tübingen University of Tübingen Tübingen 72074 Germany Quantitative Biology Center University of Tübingen Tübingen 72074 Germany Biomolecular Interactions Max Planck Institute for Developmental Biology Tübingen 72076 Germany

Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences University of Utrecht Utrecht 3548 CH Netherlands Netherlands Proteomics Center Utretcht 3584 CH Netherlands

CALIPHO Group SIB Swiss Institute of Bioinformatics Geneva 1015 Switzerland Department of Human Protein Science Faculty of Medicine University of Geneva Geneva 1205 Switzerland

Center for Biotechnology Bielefeld University Bielefeld 33615 Germany

Center for Proteomics and Metabolomics Leiden University Medical Center Leiden 2333 ZA Netherlands

Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M 5230 Denmark

Department of Biomedical Sciences University of Padova Padova 1 35121 Italy

Department of Mathematics and Computer Science University of Antwerp Antwerp 2020 Belgium

ELIXIR Hub Cambridge CB10 1SD UK

European Molecular Biology Laboratory European Bioinformatics Institute Cambridge CB10 1SD UK

French Proteomics Infrastructure ProFI Grenoble France

Institute of Microbiology Czech Academy of Sciences Prague 1 117 20 Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague 1 117 20 Czech Republic

Interuniversity Institute for Biostatistics and Statistical Bioinformatics Hasselt University Hasselt 3500 Belgium Center for Proteomics University of Antwerp Antwerpen 2000 Belgium Applied Bio and Molecular Systems VITO Mol BE 2400 Belgium

Medical Bioinformatics Medizinisches Proteom Center Ruhr University Bochum Bochum 44801 Germany

National Bioinformatics Infrastructure Sweden SciLifeLab Department of Immunotechnology Lund University Lund 223 62 Sweden

Netherlands Metabolomics Centre Utrecht 3511 GC Netherlands Dutch Techcentre for Life Sciences ELIXIR NL Utrecht 3511 GC Netherlands

Proteome Informatics Group SIB Swiss Institute of Bioinformatics Geneva 1015 Switzerland Computer Science Department University of Geneva Geneva 1205 Switzerland

ProteoRed Proteomics Unit Centro Nacional de Biotecnología Madrid 28049 Spain

VIB UGent Center for Medical Biotechnology Ghent 9052 Belgium Department of Biochemistry Ghent University Ghent 9000 Belgium

Citace poskytuje Crossref.org

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$a Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.
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$a Laukens, Kris $u Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium.
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$a Levander, Fredrik $u National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Immunotechnology, Lund University, Lund, 223 62, Sweden.
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$a Lisacek, Frederique $u Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1015, Switzerland. Computer Science Department, University of Geneva, Geneva, 1205, Switzerland.
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$a Novak, Petr $u Institute of Microbiology, Czech Academy of Sciences, Prague 1, 117 20, Czech Republic.
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$a Palmblad, Magnus $u Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands.
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$a Pühler, Alfred $u Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
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$a Schwämmle, Veit $u Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, 5230, Denmark.
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$a Valkenborg, Dirk $u Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, 3500, Belgium. Center for Proteomics, University of Antwerp, Antwerpen, 2000, Belgium. Applied Bio & Molecular Systems, VITO, Mol, BE-2400, Belgium.
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$a van Rijswijk, Merlijn $u Netherlands Metabolomics Centre, Utrecht, 3511 GC, Netherlands. Dutch Techcentre for Life Sciences / ELIXIR-NL, Utrecht, 3511 GC, Netherlands.
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$a Vondrasek, Jiri $u Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 1, 117 20, Czech Republic.
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$a Eisenacher, Martin $u Medical Bioinformatics, Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, 44801, Germany.
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$a Martens, Lennart $u VIB-UGent Center for Medical Biotechnology, Ghent, 9052, Belgium. Department of Biochemistry, Ghent University, Ghent, 9000, Belgium.
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$a Kohlbacher, Oliver $u Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, 72074, Germany. Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, 72074, Germany. Quantitative Biology Center, University of Tübingen, Tübingen, 72074, Germany. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
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