Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2024-11-18 DOI:10.1093/nar/gkae991

Charles Hawkins, Bo Xue, Yasmin Farida, Gabrielle Wyatt, Philipp Zerbe, Seung Y Rhee

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引用次数: 0

Abstract

The Plant Metabolic Network (PMN) is a free online database of plant metabolism available at https://plantcyc.org. The latest release, PMN 16, provides metabolic databases representing >1200 metabolic pathways, 1.3 million enzymes, >8000 metabolites, >10 000 reactions and >15 000 citations for 155 plant and green algal genomes, as well as a pan-plant reference database called PlantCyc. This release contains 29 additional genomes compared with PMN 15, including species listed by the African Orphan Crop Consortium and nonflowering plant species. Furthermore, 52 new enzymes with experimentally supported function information have been included in this release. The single-species databases contain a combination of experimental information from the literature and computationally predicted information obtained through PMN's database generation pipeline for a single species, while PlantCyc contains only experimental information but for any species within Viridiplantae. PMN is a comprehensive resource for querying, visualizing, analyzing and interpreting omics data with metabolic knowledge. It also serves as a useful and interactive tool for teaching plant metabolism.

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植物代谢网络 16：扩大代表性不足的植物组别和实验支持的酶数据。

植物代谢网络（PMN）是一个免费的植物代谢在线数据库，网址是 https://plantcyc.org。最新发布的 PMN 16 提供了代表 155 个植物和绿藻基因组的 >1200 个代谢途径、130 万个酶、>8000 个代谢物、>10000 个反应和 >15000 个引文的代谢数据库，以及一个名为 PlantCyc 的泛植物参考数据库。与第 15 版相比，本版增加了 29 个基因组，包括非洲孤儿作物联盟（African Orphan Crop Consortium）列出的物种和非开花植物物种。此外，该版本还收录了 52 种具有实验支持功能信息的新酶。单物种数据库包含文献中的实验信息和通过 PMN 数据库生成管道获得的单物种计算预测信息，而 PlantCyc 仅包含实验信息，但适用于病毒植物内的任何物种。PMN 是利用代谢知识查询、可视化、分析和解释 omics 数据的综合资源。它还是植物新陈代谢教学的有用互动工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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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.