Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System

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 G...

Full description

Saved in:
Bibliographic Details
Published in:Trends in microbiology (Regular ed.) 2015-11, Vol.23 (11), p.730-741
Main Authors: Markowitz, Victor M, Chen, I-Min A, Chu, Ken, Pati, Amrita, Ivanova, Natalia N, Kyrpides, Nikos C
Format: Article
Language:English
Subjects:
comparative genome analysis
Computational Biology
Database Management Systems
Databases, Genetic
Genome, Microbial - genetics
Genomics - methods
Internal Medicine
Metagenome - genetics
metagenomics
microbial genomics
Models, Molecular
Software
Statistics as Topic
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0966-842X
1878-4380
DOI:10.1016/j.tim.2015.07.012