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

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-26 DOI:10.1093/nar/gkae1063

Venkata Chandrasekhar, Kohulan Rajan, Sri Ram Sagar Kanakam, Nisha Sharma, Viktor Weißenborn, Jonas Schaub, Christoph Steinbeck

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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 are 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 have been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.

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椰子 2.0：对开放式天然产品数据库进行全面检查和整理

COCONUT （COlleCtion of Open Natural prodUcTs）数据库于 2021 年推出，是一个公开的天然产品数据集的汇总，自此成为最大的开放式天然产品数据库之一。除了天然产物的化学结构外，COCONUT 还包含有关天然产物的名称和同义词、物种和生物体部分的信息，以及有关收集相应样本的地理信息和文献参考（如有）。COCONUT 可通过 https://coconut.naturalproducts.net 公开访问。用户可以搜索文本信息，并进行结构、亚结构和相似性搜索。COCONUT 中的数据可以 SDF、CSV 和数据库转储形式批量下载。访问数据的网络应用程序是开源的。在此，我们将介绍 COCONUT 2.0，其网络应用程序已完全重写，数据也经过了新的组装和广泛的整理。新功能包括用户提交数据和以各种方式促进社区整理。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.