The LOTUS initiative for open knowledge management in natural products research

LOTUS
Natural Products
Open Science
Wikidata
Knowledge Graph
Authors
Affiliations

Adriano Rutz

University of Geneva ROR logo

Maria Sorokina

Friedrich-Schiller-University Jena ROR logo

Jakub Galgonek

Czech Academy of Sciences ROR logo

Daniel Mietchen

Ronin Institute ROR logo

Leibniz Institute of Freshwater Ecology and Inland Fisheries ROR logo

University of Virginia ROR logo

Egon Willighagen

Maastricht University ROR logo

Arnaud Gaudry

University of Geneva ROR logo

James G. Graham

University of Illinois at Chicago ROR logo

Ralf Stephan

Ontario Institute for Cancer Research ROR logo

Roderic Page

University of Glasgow ROR logo

Jiří Vondrášek

Christoph Steinbeck

Friedrich-Schiller-University Jena ROR logo

Guido F. Pauli

University of Illinois at Chicago ROR logo

Jean-Luc Wolfender

University of Geneva ROR logo

Jonathan Bisson

University of Illinois at Chicago ROR logo

Pierre-Marie Allard

University of Geneva ROR logo

University of Fribourg ROR logo

Published

May 26, 2022

Doi
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.

References

Rutz, Adriano, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G Graham, et al. 2022. “The LOTUS Initiative for Open Knowledge Management in Natural Products Research.” eLife 11 (May). https://doi.org/10.7554/elife.70780.