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.
Highlights
Perspective pubs.acs.org/ac NMR Markup Language (nmrML): A Community Supported Open Data Standard for the Description, Storage, and Exchange of N uclear magnetic resonance (NMR) 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 controlled vocabulary (CV) referencing mechanism and basic XML architecture was inspired by mass spectrometry markup language, the Proteomics Standard Initiatives (PSI) standard mass spectrometry data format used in proteomics and metabolomics.[16]
Summary
Perspective pubs.acs.org/ac nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. The need for an open NMR data standard covering the free induction decay (FID) to support data reproducibility has been acknowledged.[1] As instrument vendors typically provide the data processing software and produce evolving data formats together with the instrument hardware, developers of third party NMR analysis software often need to devote considerable effort into reading and writing these vendorspecific formats This applies both to commercial software and to community developed open-source tools such as the BATMAN R package,[2] Bayesil,[3] NMRProcFlow,[4] rNMR5 and MetaboLab.[6] With the recent termination of the Agilent/Varian NMR spectrometer range, the question of long-term readability of discontinued vendor formats has become paramount for a growing NMR community. While JCAMP-DX is likely to remain in use for NMR data capture for many years, it is clear that alternative approaches, such as XML or JavaScript Object Notation (JSON) with peermaintained ontologies, would be beneficial
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