GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-11-05 DOI:10.1093/nar/gkae1057

Guomei Fan, Qinglan Sun, Yan Sun, Dongmei Liu, Shiwen Li, Min Li, Qi Chen, Fang Wang, Ohkuma Moriya, Takashi Itoh, Hiroko Kawasaki, Yajing Yu, Man Cai, Song-Gun Kim, Jung-Sook Lee, Juncai Ma, Linhuan Wu

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Abstract

Microbial culture collections play a crucial role in the collection, maintenance, and distribution of quality-assured living microbial strains, along with their associated phenotypic and omics data. To enhance the find-able, accessible, interoperable, and re-usable (FAIR) data utilization of microbial resources, the World Data Center for Microorganisms (WDCM) has developed the Global Catalogue of Microorganisms (GCM) and the Global Catalogue of Type Strains (gcType). These platforms provide interactive interfaces for cataloging the holdings of collections, along with detailed annotations of type strain genomes and curated metadata, including ecosystems, growth conditions, and collection locations. The system maximizes the scientific impact of microbial resources and culture collections through an integrated data mining tool that links strain- and species-related information from various public resources. Currently, the GCM and gcType include 574 422 strains from 154 culture collections across 51 countries and regions, along with 25 980 genomes from type species. Additionally, 2 702 655 articles and 103 337 patents are integrated with these microbial resources. The system supports microbial taxonomic research and provides evidence for implementing the Nagoya Protocol in the field of microbial resources and their digital sequence information (DSI). Access is freely available at gcm.wdcm.org and gctype.wdcm.org.

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2024 年的 GCM 和 gcType：微生物菌株和基因组数据的综合资源。

在收集、维护和分发有质量保证的活体微生物菌株及其相关表型和组学数据方面，微生物培养物收藏发挥着至关重要的作用。为了提高微生物资源的可查找、可访问、可互操作和可重复使用（FAIR）数据利用率，世界微生物数据中心（WDCM）开发了全球微生物目录（GCM）和全球类型菌株目录（gcType）。这些平台提供了互动式界面，用于对收藏的藏品进行编目，同时还提供了类型菌株基因组的详细注释和经过策划的元数据，包括生态系统、生长条件和收藏地点。该系统通过综合数据挖掘工具，将各种公共资源中与菌株和物种相关的信息联系起来，从而最大限度地发挥微生物资源和培养物收藏的科学影响。目前，GCM 和 gcType 包括来自 51 个国家和地区 154 个培养物保藏中心的 574 422 株菌株，以及 25 980 个类型物种的基因组。此外，这些微生物资源还整合了 2 702 655 篇文章和 103 337 项专利。该系统支持微生物分类研究，并为在微生物资源及其数字序列信息（DSI）领域实施《名古屋议定书》提供证据。可通过 gcm.wdcm.org 和 gctype.wdcm.org 免费访问。

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.