PATRIC: The Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

Published on 2011-09-07

Joseph J. Gillespie, Alice R. Wattam, Stephen A. Cammer, Joseph Gabbard, Maulik P. Shukla, Oral Dalay, Timothy Driscoll, Deborah Hix, Shrinivasrao P. Mane, Chunhong Mao, Eric K. Nordberg, Mark Scott, Julie R. Schulman, Eric E. Snyder, Daniel E. Sullivan, Chunxia Wang, Andrew Warren, Kelly P. Williams, Tian Xue, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Rebecca Will, Ronald W. Kenyon, and Bruno W. Sobral (2011). “PATRIC: The Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species”Infect. Immun 79 (11): 4286-98. doi:10.1128/IAI.00207-11.   PMC 3257917.   PMID 21896772.

Abstract

Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious disease research. Specifically, PATRIC provides scientists with 1. a comprehensive bacterial genomics database, 2. a plethora of associated data relevant to genomic analysis, and 3. an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary focus of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: ‘Organisms, Genomes and Comparative Genomics’ and ‘Recurrent Integration of Community-Derived Associated Data’. Additionally, we present two experimental designs typical of bacterial genomics research and execute both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary is provided of PATRIC’s outreach activities, collaborative endeavors, and future research directions.

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