Natural Products Magnetic Resonance Database (NP-MRD) Phase II

About This Grant

PROJECT SUMMARY/ABSTRACT Since its launch in 2021, the Natural Products Magnetic Resonance Database (NP-MRD, https://np-mrd.org) has become the largest open repository of NMR data on natural products (NPs) as well as the largest collection of general information (nomenclature, structure, biology, chemistry) about NPs in the world. The NP-MRD contains substantial amounts of different types of NMR data including raw NMR data (free induction decays or FIDs), predicted NMR data and literature-derived NMR information (chemical shift assignments, coupling constants). The NMR data in the NP-MRD includes 15,000 sets of experimental NMR spectra (for 3200 NPs), 411,000 simulated NMR spectra (for 21,000 NPs) obtained from literature-derived NMR assignments, and 5.1 million predicted NMR spectra (for all 282,000 NPs). Much of the raw NMR data in the NP-MRD is there due to a concerted effort by NP-MRD, together with the Journal of Natural Products (JNP), to encourage raw data deposition of NMR data used to support novel structure elucidation. For the second phase of the NP-MRD (2025- 2030) we will build on the momentum created in the first phase. Specifically, we will optimize current operations and continue ongoing expansion of both the database content and utility. A major emphasis will be on streamlining NP-MRD operations such that most of its operations will require little human intervention. For example, raw data deposition formerly required two NP-MRD staff in two different locations to interact with the deposited data, and with the depositor. Today, raw data deposition goes automatically into a parser, a set of quality checks and straight into the NP-MRD repository with no human intervention unless (rare) problems occur with the data. Other functions being streamlined, include centralized processes to query, enter and assess NP- MRD data, better processes to annotate NP structures, tools to more efficiently gather biological, medicinal, structural, chemical shift and assignment data from the published literature, as well as workflows to correct entries, remove duplicates and improve accuracy. In terms of data content and utility expansion, major efforts will be undertaken to increase user deposition rates, support the deposition, integration and federation of mass spectrometry (MS) data for NPs into the NP-MRD, implement faster, more “intelligent” NMR, multi-spectral (NMR+MS+CCS+RT) and multi-database (GNPS, MoNA, MassBank, HMDB, FooDB) searches, support more accurate chemical shift, J-coupling and other kinds of “observables” prediction, and create new tools to support automated computer-aided NP structure elucidation (CASE) and dereplication. These streamlining, optimization and database expansion efforts are being done to ensure long-term sustainability of the NP-MRD by making operations cheaper, more automated, more useful and more valuable to the NP community. Outreach to other NP journals and to the NP community will be further expanded, with the expectation that these efforts will triple the data deposition rate to the NP-MRD by 2030, increase community buy-in, increase grant or co-funding support, attract paying subscribers and ensure long-term sustainability of the NP-MRD.