nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data

Autor: Masashi Yokochi, Matthias S. Klein, Daniel J. Jacob, Christian Ludwig, Andrea Porzel, Kenneth Haug, Ian A. Lewis, Arturas Grauslys, Luis F. de Figueiredo, Reza M. Salek, Andrew R. Jones, Martin Larralde, David S. Wishart, Julian L. Griffin, Jie Hao, Timothy M. D. Ebbels, Joseph A. Cruz, Jason R. Grant, Ulrich L. Günther, Steffen Neumann, Daniel Schober, Philippe Rocca-Serra, Christoph Steinbeck, John M. Easton, Annick Moing, Ana Marcu, Naohiro Kobayashi, Catherine Deborde, Mark R. Viant, Claudio Luchinat, Michael Wilson, Antonio Rosato
Přispěvatelé: Commission of the European Communities, European Molecular Biology Laboratory, Leibniz Institute of Plant Biochemistry (IPB), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, University of Alberta, European Molecular Biology Laboratory (EMBL), Oxford e-Research Centre [Oxford], University of Oxford [Oxford], University of Birmingham, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Biological Sciences, University of Calgary, Institute of Integrative Biology, Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Osaka University, Department of Bioorganic Chemistry, Leibniz Institute for Plant Biochemistry, Department of Biochemistry, University of Cambridge [UK] (CAM), School of Biosciences, University of Birmingham [Birmingham]
Rok vydání: 2017
Předmět:
Zdroj: Analytical Chemistry
Analytical Chemistry, American Chemical Society, 2018, 90 (1), pp.649-656. ⟨10.1021/acs.analchem.7b02795⟩
ISSN: 1520-6882
0003-2700
DOI: 10.1021/acs.analchem.7b02795
Popis: UMR BFP - Equipe Métabolisme; International audience; NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters and, where available, spectral metadata such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex bio-mixtures i.e. metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker and Agilent/Varian vendor formats. In addition, easy-to-use web-based spectral viewing, processing and spectral assignment tools that read and write nmrML have been developed. Software libraries and web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g. serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI) and we here encourage user participation and feedback to increase usability and make it a successful standard.
Databáze: OpenAIRE
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