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Schober D, Jacob D, Wilson M, et al. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. Anal Chem. 2017;90(1):649-656doi: 10.1021/acs.analchem.7b02795.
Schober, D., Jacob, D., Wilson, M., Cruz, J. A., Marcu, A., Grant, J. R., Moing, A., Deborde, C., de Figueiredo, L. F., Haug, K., Rocca-Serra, P., Easton, J., Ebbels, T. M. D., Hao, J., Ludwig, C., Günther, U. L., Rosato, A., Klein, M. S., Lewis, I. A., Luchinat, C., Jones, A. R., Grauslys, A., Larralde, M., Yokochi, M., Kobayashi, N., Porzel, A., Griffin, J. L., Viant, M. R., Wishart, D. S., Steinbeck, C., Salek, R. M., & Neumann, S. (2018). nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. Analytical chemistry, 90(1), 649-656. https://doi.org/10.1021/acs.analchem.7b02795
Schober, Daniel, et al. "nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data." Analytical chemistry vol. 90,1 (2018): 649-656. doi: https://doi.org/10.1021/acs.analchem.7b02795
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. Anal Chem. 2018 Jan 02;90(1):649-656. doi: 10.1021/acs.analchem.7b02795. Epub 2017 Dec 14. PMID: 29035042.
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Anal Chem. 2018 Jan 02;90(1):649-656. doi: 10.1021/acs.analchem.7b02795. Epub 2017 Dec 14.

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

Analytical chemistry

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, John Easton, Timothy M D Ebbels, Jie Hao, Christian Ludwig, Ulrich L Günther, 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, Mark R Viant, David S Wishart, Christoph Steinbeck, Reza M Salek, Steffen Neumann

Affiliations

  1. Leibniz Institute of Plant Biochemistry , Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany.
  2. INRA, Univ. Bordeaux , UMR1332 Fruit Biology and Pathology, Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA Bordeaux, 71 av Edouard Bourlaux, F-33140 Villenave d'Ornon, France.
  3. Departments of Computing Sciences and Biological Sciences, University of Alberta , Edmonton, Canada T6G 2E8.
  4. European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.
  5. University of Oxford , e-Research Centre1, 7 Keble Road, Oxford OX1 3QG, U.K.
  6. School of Engineering, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.
  7. Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London , London, SW7 2AZ, U.K.
  8. Institute of Metabolism and Systems Research, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.
  9. Institute of Cancer and Genomic Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.
  10. Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence , 50019 Sesto Fiorentino, Florence, Italy.
  11. Department of Biological Sciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
  12. Institute of Integrative Biology, University of Liverpool , Bioscience Building, Crown Street, Liverpool L69 7ZB, U.K.
  13. Ecole Normale Supérieure Paris-Saclay , 61 Avenue du Président Wilson, 94230 Cachan, France.
  14. Institute for Protein Research (IPR), Osaka University , 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan.
  15. Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry , 06120 Halle (Saale), Germany.
  16. Department of Biochemistry, University of Cambridge , Downing Site, Cambridge CB2 1QW, U.K.
  17. School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.

PMID: 29035042 DOI: 10.1021/acs.analchem.7b02795

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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