nmrML: a community supported open data standard for the description, storage, and exchange of NMR data.
ROSATO, Antonio
Università degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
Università degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
LUCHINAT, Claudio
Università degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
< Réduire
Università degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
Langue
en
Article de revue
Ce document a été publié dans
Analytical Chemistry. 2018, vol. 90, n° 1, p. 649-656
American Chemical Society
Résumé en anglais
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 ...Lire la suite >
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.< Réduire
Mots clés
XML
MSI
metabolomics
Mots clés en anglais
nuclear magnetic resonance spectroscopy
NMR
open source
data standard
ontology
controlled vocabulary
validation
workflows
Project ANR
Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation
Origine
Importé de halUnités de recherche