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

Maria Sorokina

Friedrich-Schiller-University Jena

Jakub Galgonek

Czech Academy of Sciences

Daniel Mietchen

Ronin Institute

Leibniz Institute of Freshwater Ecology and Inland Fisheries

University of Virginia

Egon Willighagen

Maastricht University

Arnaud Gaudry

University of Geneva

James G. Graham

University of Illinois at Chicago

Ralf Stephan

Ontario Institute for Cancer Research

Roderic Page

University of Glasgow

Jiří Vondrášek

Christoph Steinbeck

Friedrich-Schiller-University Jena

Guido F. Pauli

University of Illinois at Chicago

Jean-Luc Wolfender

University of Geneva

Jonathan Bisson

University of Illinois at Chicago

Pierre-Marie Allard

University of Geneva

University of Fribourg

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.