title: PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.
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 (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim 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: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of 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 of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.
authors: Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061, USA.
authors: Joseph J
authors: JJ
authors: Gillespie
authors: Alice R
authors: AR
authors: Wattam
authors: Stephen A
authors: SA
authors: Cammer
authors: Joseph L
authors: JL
authors: Gabbard
authors: Maulik P
authors: MP
authors: Shukla
authors: Oral
authors: O
authors: Dalay
authors: Timothy
authors: T
authors: Driscoll
authors: Deborah
authors: D
authors: Hix
authors: Shrinivasrao P
authors: SP
authors: Mane
authors: Chunhong
authors: C
authors: Mao
authors: Eric K
authors: EK
authors: Nordberg
authors: Mark
authors: M
authors: Scott
authors: Julie R
authors: JR
authors: Schulman
authors: Eric E
authors: EE
authors: Snyder
authors: Daniel E
authors: DE
authors: Sullivan
authors: Chunxia
authors: C
authors: Wang
authors: Andrew
authors: A
authors: Warren
authors: Kelly P
authors: KP
authors: Williams
authors: Tian
authors: T
authors: Xue
authors: Hyun Seung
authors: HS
authors: Yoo
authors: Chengdong
authors: C
authors: Zhang
authors: Yan
authors: Y
authors: Zhang
authors: Rebecca
authors: R
authors: Will
authors: Ronald W
authors: RW
authors: Kenyon
authors: Bruno W
authors: BW
authors: Sobral
mesh_terms: D001419:Bacteria / Q000472:pathogenicity*; D001424:Bacterial Infections / Q000382:microbiology*; D019295:Computational Biology; D016208:Databases, Factual; D023281:Genomics; D006801:Humans