The LOTUS initiative for open knowledge management in natural products research

Abstract

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.

Inventa: a computational tool to discover chemical novelty in natural extracts libraries

“…By default, the weight of each fraction is equal; it can be pondered by the user depending on the needs. For the calculation of this value, the clean taxonomic information (based on the Open Tree of Life , OTL) is retrieved from the metadata table and used to query the NPs occurrences reported in the LOTUS initiative (Rutz et al, 2022). The LC represents a rough estimation of the literature knowledge on a given extract in terms of reported compounds.…”

“…The SIRIUS .mgf file exported from MZmine (using the SIRIUS export module) that contains MS1 and MS2 information was processed with SIRIUS (v 5.5.5) command-line tools on a Linux server (Dührkop et al, 2019). The molecular formula and metabolite database used for SIRIUS includes NPs from LOTUS (Rutz et al, 2022) and the Dictionary of Natural Products (DNP). The parameters were set as follows: Possible ionizations : [M+H] + , [M+NH 4 ] + , [M-H 2 O+H] + , [M+K] + , [M+Na] + ,[M-4H2O+H] + ; Instrument profile : Orbitrap; mass accuracy : 5 ppm for MS 1 and 7 ppm for MS 2 , database for molecular formulas and structures:BIO and custom databases (LOTUS, DNP), maximum m/z to compute : 1000.…”

Integrative omics approaches for biosynthetic pathway discovery in plants

“…It is estimated that, until now, only 6% of the total plant metabolic structural diversity has been cataloged in the Dictionary of Natural Product (DNP https://www.dnp.chemnetbase.com/ faces/chemical/ChemicalSearch.xhtml). 69 Here, we note that the recently introduced LOTUS (naturaL prOducT occUrrence databaSe) 70 As the classical reductive approach (experimental and targeted approaches) to characterize metabolites is laborious and time-consuming, untargeted metabolomics using mass spectrometry (MS) has immense potential in performing widescreen proling of specialized metabolites and identifying an unprecedented number of metabolic classes from crude extracts. 71,72 High-throughput identication of metabolites from multiple sources, for instance, leaf, root, soil, volatiles, etc., have fueled the discovery of biosynthetic pathways by enabling the identication of key changes in the metabolite proles.…”

Chemoinformatics and Artificial Intelligence Colloquium: Progress and Challenges to Develop Bioactive Compounds

“…Similarly, the low amount of data associated with NPs has limited the potential applications of ML and DL in the study of naturally occurring compounds. Initiatives such as the NuBBE DB , a virtual database of NPs and derivatives from the Brazilian biodiversity [63,64], have paved the way for developing new NP databases and projects like LOTUS [65] for NP storage, search, and analysis. With the data collected to date, different applications have been proposed using chemoinformatics [66] and AI [31].…”