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

Research output: Contribution to journalArticlepeer-review

Authors

  • Daniel Schober
  • Daniel Jacob
  • Michael Wilson
  • Joseph A. Cruz
  • Ana Marcu
  • Jason R. Grant
  • Annick Moing
  • Catherine Deborde
  • Luis F. De Figueiredo
  • Kenneth Haug
  • Philippe Rocca-Serra
  • Timothy M.D. Ebbels
  • Jie Hao
  • Antonio Rosato
  • Matthias S. Klein
  • Ian A. Lewis
  • Claudio Luchinat
  • Andrew R. Jones
  • Arturas Grauslys
  • Martin Larralde
  • Masashi Yokochi
  • Naohiro Kobayashi
  • Andrea Porzel
  • Julian L. Griffin
  • David S. Wishart
  • Christoph Steinbeck
  • Reza M. Salek
  • Steffen Neumann

External organisations

  • Leibniz Institute of Plant Biochemistry
  • INRA Bordeaux-Aquitaine
  • University of Alberta
  • THE WELLCOME TRUST
  • Oxford University
  • Imperial College London
  • University of Florence
  • University of Calgary
  • University of Liverpool
  • Ecole Normale Supérieure Paris-Saclay
  • Osaka University
  • University of Cambridge

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.

Details

Original languageEnglish
Pages (from-to)649-656
Number of pages8
JournalAnalytical Chemistry
Volume90
Issue number1
Early online date16 Oct 2017
Publication statusPublished - 2 Jan 2018

Keywords

  • Journal Article

ASJC Scopus subject areas