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.

DrugBank 5.0: a major update to the DrugBank database for 2018

“…In response to these needs, all of DrugBank’s chemical structures are now accessible in canonical SMILES, SDF, MOL, PDB, InChI and InChIKey formats. Furthermore, all experimentally observed and theoretically predicted MS/MS, GC-MS and NMR spectra are stored and downloadable in mzML ( 7 ) and nmrML ( 8 ) formats and all MS/MS and GC-MS spectra are assigned SPLASH keys ( 6 ) for rapid spectral querying and matching. Likewise, all sequence (DNA and protein) data are stored in FASTA format and all remaining textual data are stored in XML and JSON format.…”

“…Additionally, DrugBank's curation team has greatly improved the quality and consistency of all existing drug indications, enhanced the information on drug-drug and drug-food interactions, filled in data gaps on more than 600 existing drugs and greatly improved the quality and quantity of drug-target binding data. Major improvements to the spectral viewing and spectral search tools, spectral data formats (compatible with SPLASH ( 6 ), mzML ( 7 ) and nmrML ( 8 )), chemical taxonomies, chemical ontologies ( 9 ), as well as text and structure searching/matching have also been made. Further details on the additions and enhancements made to DrugBank 5.0 are described below.…”

Integrated omics: tools, advances and future approaches

“…Similarly, a state-of-theart data-independent acquisition carried out via SWATH MS Gold Standard data set was made available (Röst et al 2014) to the proteomics research community. Examples of such efforts in lipidomics include harmonization and interoperability of metabolomics standards (Bowden et al 2017) and data sharing, the description, storage and exchange of NMR-based metabolomics efforts (Schober et al 2018). In the absence of robust statistical treatment and measures, investigators are liable to employ 'p-hacking' (investigators select data or statistical analyses until non-significant results become significant).…”

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

“…simply by providing a MetaboLights accession number), leading to the capability to re-analyze data and compare the results with the original publication findings. Furthermore, it demonstrates the value of standardised dataset descriptions such as nmrML (43) and ISA format (44,45) for representing NMR based studies, as well as the potential of the VRE to foster reproducibility.…”