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COCONUT 2.0: A comprehensive overhaul and curation of the collection of open natural products database

16 October 2024, Version 2
Working Paper
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species, and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected, and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT is available for bulk download as SDF, CSV, and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data has been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.

Keywords

Natural Products
Database
Metabolites
Chemical Structure Curation
Open Data
FAIR
Community Curation

Supplementary weblinks

Title
Description
Actions
Title
COCONUT
Description
A comprehensive platform facilitating natural product research through data and tools while upholding FAIR principles for Research Data Management.
Actions
View
Title
COCONUT GitHub
Description
COCONUT (COlleCtion of Open Natural prodUcTs): Code base of COCONUT web application
Actions
View

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Version History

Oct 16, 2024 Version 2

Version Notes

We have made several key updates to improve the manuscript and the COCONUT 2.0 database. The export functionality has been enhanced to include comprehensive metadata, such as species, evidence, and data sources, available in both CSV and SDF formats to facilitate easier access to the full range of data. A feature comparison table has been added to the manuscript to clearly illustrate the differences between COCONUT versions 1.0 and 2.0. Additionally, we have expanded the discussion on the scoring system used to classify natural products, providing specific examples of non-natural products and visualizing the distribution of NPLikeness and annotation scores. This information is included in both the main manuscript and supplementary materials, along with cautionary statements regarding data quality to ensure transparency in the classification process.

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License

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CC
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BY
The content is available under CC BY 4.0 [opens in a new tab]

DOI

10.26434/chemrxiv-2024-fxq2s-v2
D O I: 10.26434/chemrxiv-2024-fxq2s-v2 [opens in a new tab]

Funding

German Research Foundation
239748522
German Federal Ministry of Education and Research
03ZU1214OA

Author’s competing interest statement

The author(s) have declared they have no conflict of interest with regard to this content

Ethics

The author(s) have declared ethics committee/IRB approval is not relevant to this content

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