What is NP-MRD?
The NP-MRD (Natural Products Magnetic Resonance Database) is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD accepts NMR data and associated metadata from newly undertaken NP studies. The NP-MRD accepts raw (time domain data, processed spectra, assigned chemical shifts, J-couplings, RDCs, etc.), and meta-data (structures, sources, methods, taxonomy, geospatial data, etc) from natural products ranging from purified substances to crude extracts, in all major solvents. The NP-MRD includes NPs such as vitamins, minerals, and probiotics as well as small molecules derived from plants, fungi, bacteria, marine organisms, or animals. The NP-MRD accepts, converts, and stores all major vendor NMR formats and all major NMR data exchange formats from all common NMR experiments as well as new/uncommon NMR experiments or data sets. The NP-MRD has an intuitive user interface for spectra/structure deposition, retrieval, search, and analysis. Data deposition is fast (<5 min/per spectrum), easy and intuitive, and aided by online assignment and online spectra/structure visualization tools. Structure and assignment validation reports are generated within 5 minutes of deposition and value-added data reports are provided to users within 24 hours of deposition, including high-quality DFT calculations of chemical shifts for a deposited structure. Data integrity and data quality are ensured by extensive curation efforts and the use of an objective ranking scale for all deposited data.
- World’s largest natural products NMR database, with every entry checked for its natural product origins.
- Contains detailed taxonomic/species information (i.e., compound provenance) about all compounds in the database.
- Detailed, mostly hand-written descriptions for every compound in the database.
- Comprehensive chemical ontology for all compounds in the database.
- Detailed (measured and calculated) physico-chemical data for every compound in the database.
- 3D structures and 3D structure files for every compound in the database.
- The NP-MRD is fully FAIR compliant (something that no other NMR database is).
- Extensive support for user deposition of 1D and 2D NMR spectral data and NMR assignment data.
- Contains accurately (ML and DFT) predicted 1H, 13C and J-coupling data.
- Provides NMR data for multiple (10) NMR spectrometer frequencies.
- State-of-the-art structure visualization tools.
- State-of-the-art spectral visualization tools.
- Support for all major NMR data exchange formats.
- Support of all major chemical data exchange formats.
- Wide range of sophisticated structure, MW and spectral search functions.
- Supports extensive data filtering and selection.
- Extensive support for a wide variety of data downloads.
- Extensive hyperlinks to many databases.
- Largest collection of literature references for any NMR database.
- Objective rating of the quality of all of its assignment depositions.
- Provides a data quality report for all of its spectral depositions.
- >20,000 unique compound entries that are not found in any NMR database.
The NP-MRD is FAIR. Specifically it is:
F1. (meta)data are assigned a globally unique and eternally persistent identifier.
All data and metadata in the NP-MRD is assigned a 7 digit globally unique NP identifier. This identifier is searchable within the database and associated with all data in the online database. Furthermore, the identifier is associated with all data downloadable from the database.
F2. data are described with rich metadata.
All data in the NP-MRD are described with rich metadata. Every compound and spectrum is described in detail. Structures, names, synonyms, biological sources (if available), descriptions, experimental details and other relevant data are all attached to the referential data. Additionally, scientific references are provided for each entry.
F3. meta)data are registered or indexed in a searchable resource.
All the data and metadata in the NP-MRD is indexed, viewable and registered through the NP-MRD online database at www.np-mrd.org
F4. metadata specify the data identifier.
All metadata entries in the NP-MRD are directly linked to the NP-MRD (NP) identifier and associated NMR spectra.
A1 (meta)data are retrievable by their identifier using a standardized communications protocol.
All data and metadata in the NP-MRD are retrievable from their NP identifier through the NP-MRD website. Similarly, all data in the NP-MRD may be downloaded in JSON and/or nmrML format via the NP-MRD’s download section through a standard internet communications protocol
A1.1 the protocol is open, free, and universally implementable.
The NP-MRD website is open and free and its data download operation is compatible with all modern web browsers. The NP-MRD’s downloadable data is in a format (nmrML) that is universally readable.
A1.2 the protocol allows for an authentication and authorization procedure, where necessary.
No authentication or authorization is required to access or download the NP-MRD’s data. Authorization is required to upload data to the NP-MRD.
A2 metadata are accessible, even when the data are no longer available.
All of the NP-MRD’s metadata are linked or linkable to more permanent data sources (PubMed, HMDB, NPAtlas, etc.). The availability of freely downloadable data (and metadata) for the NP-MRD ensures that its metadata will exist and be accessible for beyond the lifetime of the database.
I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.
All textual data and metadata in the NP-MRD are written in English, all spectral data is in the nmrML exchange format, all images are stored in PNG format, all nomenclature for compounds and spectral data follows standard ontologies or vocabularies used to describe these entities.
I2. (meta)data use vocabularies that follow FAIR principles.
All data and metadata in the NP-MRD use ontologies and vocabularies that are open, findable, accessible, interoperable and re-usable.
I3. (meta)data include qualified references to other (meta)data.
All data and metadata in the NP-MRD are fully referenced with detailed descriptions of their provenance and sources.
R1. meta(data) have a plurality of accurate and relevant attributes.
All data and metadata in the NP-MRD deposited by its curation team have been carefully curated and vetted by multiple skilled curators. All data deposited into the NP-MRD have been automatically checked for accuracy and consistency using comprehensive data checking software and all user depositions have received depositor assurances that they are correct and accurate. All data in the NP-MRD have attributes that are relevant, up-to-date and accurate to the best of the NP-MRD curation team’s knowledge.
R1.1. (meta)data are released with a clear and accessible data usage license.
All data and metadata in the NP-MRD are released under the Creative Commons (CC) 4.0 License Suite according to the Attribution (BY) and Non-commercial (NC) licensing conditions.
R1.2. (meta)data are associated with their provenance.
All data and metadata in the NP-MRD have detailed descriptions of their provenance and sources
R1.3. (meta)data meet domain-relevant community standards.
The data and metadata in the NP-MRD has undergone extensive peer review by members of the NMR and natural products community. The data in the NP-MRD has met the standards for publication in peer-reviewed scientific journals and international scientific conferences.
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
This means that our data can be used in derivative works as long as proper attribution is given to the source of the data, but these derivative works may not be used for commercial purposes.