Biosciences Computing, Computing Research Division, Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Biosciences Computing, Computing Research Division, Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Trends Microbiol. 2015 Nov;23(11):730-741. doi: 10.1016/j.tim.2015.07.012. Epub 2015 Oct 14.
Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure.
IMG 系统于 2005 年 3 月推出，是一个全面的数据管理系统，支持基因组数据的多维比较分析。IMG 系统的核心是一个数据仓库，其中包含在联合基因组研究所测序的基因组和宏基因组数据集，或由科学用户提供的数据集，以及可从国家生物技术信息中心 Genbank 序列数据档案获得的公共基因组数据集。基因组和宏基因组数据集使用 IMG 的微生物基因组和宏基因组序列数据处理管道进行处理，并使用 IMG 的数据集成工具包集成到数据仓库中。微生物基因组和宏基因组应用特定的数据集市和用户界面提供对 IMG 数据和分析工具包的不同子集的访问。本文回顾了 IMG 的最初目标，强调了系统在过去 10 年中取得的关键里程碑，并讨论了一个快速扩展的系统所面临的主要挑战，特别是在预算有限、计算和数据管理基础设施有限的学术环境下维护这样一个系统的复杂性。
