Bioinformatics Analysis Tools for Studying Microbiomes at the DOE Joint Genome Institute

IF 1.8 4区综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Journal of the Indian Institute of Science Pub Date : 2023-05-30 DOI:10.1007/s41745-023-00365-w

Supratim Mukherjee, Krishnaveni Palaniappan, Rekha Seshadri, Ken Chu, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Cody Webb, Dongying Wu, Neha Varghese, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Robert M. Bowers, Antonio Pedro Camargo, Stephen Nayfach, Frederik Schulz, Simon Roux, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos C. Kyrpides, I.-Min A. Chen, T. B. K. Reddy

{"title":"Bioinformatics Analysis Tools for Studying Microbiomes at the DOE Joint Genome Institute","authors":"Supratim Mukherjee, Krishnaveni Palaniappan, Rekha Seshadri, Ken Chu, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Cody Webb, Dongying Wu, Neha Varghese, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Robert M. Bowers, Antonio Pedro Camargo, Stephen Nayfach, Frederik Schulz, Simon Roux, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos C. Kyrpides, I.-Min A. Chen, T. B. K. Reddy","doi":"10.1007/s41745-023-00365-w","DOIUrl":null,"url":null,"abstract":"<div><p>The DOE Joint Genome Institute has developed and maintains a number of computational resources and databases to help biologists perform -omics-based scientific research. In this review, we describe two of its widely used microbiome data management and analysis resources: the Genome OnLine Database (GOLD) and the Integrated Microbial Genomes (IMG). GOLD is a sequencing project and associated metadata management system. It provides a catalog of genome and metagenome projects with well-curated associated metadata which are critical for sequence data interpretation. IMG is an omics data management system enabling the comparative analysis of microbial genomes, metagenomes, and metatranscriptomics and their associated genes and functions. IMG contains close to 200,000 datasets and provides advanced search and comparative analysis tools. GOLD’s metadata are integrated into IMG to provide a better understanding of the environments and properties of each dataset. In addition to all the public data integrated, both systems support private user data submission and integration to support annotation and comparative analysis with all other data integrated into the systems. There are currently over 25,000 registered users from more than 110 countries, and the systems are also used for educational purposes across various universities around the world.\n</p></div>","PeriodicalId":675,"journal":{"name":"Journal of the Indian Institute of Science","volume":"103 3","pages":"857 - 875"},"PeriodicalIF":1.8000,"publicationDate":"2023-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s41745-023-00365-w.pdf","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of the Indian Institute of Science","FirstCategoryId":"103","ListUrlMain":"https://link.springer.com/article/10.1007/s41745-023-00365-w","RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}

引用次数: 3

Abstract

The DOE Joint Genome Institute has developed and maintains a number of computational resources and databases to help biologists perform -omics-based scientific research. In this review, we describe two of its widely used microbiome data management and analysis resources: the Genome OnLine Database (GOLD) and the Integrated Microbial Genomes (IMG). GOLD is a sequencing project and associated metadata management system. It provides a catalog of genome and metagenome projects with well-curated associated metadata which are critical for sequence data interpretation. IMG is an omics data management system enabling the comparative analysis of microbial genomes, metagenomes, and metatranscriptomics and their associated genes and functions. IMG contains close to 200,000 datasets and provides advanced search and comparative analysis tools. GOLD’s metadata are integrated into IMG to provide a better understanding of the environments and properties of each dataset. In addition to all the public data integrated, both systems support private user data submission and integration to support annotation and comparative analysis with all other data integrated into the systems. There are currently over 25,000 registered users from more than 110 countries, and the systems are also used for educational purposes across various universities around the world.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

美国能源部联合基因组研究所用于研究微生物组的生物信息学分析工具

美国能源部联合基因组研究所开发并维护了许多计算资源和数据库，以帮助生物学家进行基于组学的科学研究。在这篇综述中，我们描述了两种广泛使用的微生物组数据管理和分析资源：基因组在线数据库（GOLD）和综合微生物基因组（IMG）。GOLD是一个排序项目和相关的元数据管理系统。它提供了基因组和宏基因组项目的目录，以及精心策划的相关元数据，这些元数据对序列数据解释至关重要。IMG是一个组学数据管理系统，能够对微生物基因组、宏基因组和宏转录组学及其相关基因和功能进行比较分析。IMG包含近200000个数据集，并提供高级搜索和比较分析工具。GOLD的元数据集成到IMG中，以更好地了解每个数据集的环境和属性。除了集成所有公共数据外，这两个系统都支持私人用户数据提交和集成，以支持注释和与集成到系统中的所有其他数据的比较分析。目前有来自110多个国家的25000多名注册用户，这些系统也用于世界各地各大学的教育目的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Journal of the Indian Institute of Science MULTIDISCIPLINARY SCIENCES-

CiteScore

4.30

自引率

0.00%

发文量

期刊介绍： Started in 1914 as the second scientific journal to be published from India, the Journal of the Indian Institute of Science became a multidisciplinary reviews journal covering all disciplines of science, engineering and technology in 2007. Since then each issue is devoted to a specific topic of contemporary research interest and guest-edited by eminent researchers. Authors selected by the Guest Editor(s) and/or the Editorial Board are invited to submit their review articles; each issue is expected to serve as a state-of-the-art review of a topic from multiple viewpoints.