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

Abstract

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 biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL 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.

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Affiliated Institutions

• Leibniz Institute of Plant Biochemistry DE
• European Bioinformatics Institute GB
• University of Cambridge GB
• Biologie du Fruit et Pathologie FR
• MetaboHUB FR
• University of Birmingham GB
• Université de Bordeaux FR
• Imperial College London GB
• University of Liverpool GB
• Protein Research Foundation JP
• University of Calgary CA
• Wellcome Trust GB
• University of Oxford GB
• University of Florence IT
• The University of Osaka JP
• Interuniversity Consortium for Magnetic Resonance IT
• École Normale Supérieure Paris-Saclay FR
• Université Bourgogne Franche-Comté FR
• University of Alberta CA

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