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

By Joseph J Gillespie, A. Wattam, S. Cammer, Joseph L. Gabbard, Maulik Shukla, O. Dalay, Timothy P. Driscoll, D. Hix, S. Mane, Chunhong Mao and 15 more. Infection and Immunity, 2011

344 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ba69a521bad7a913a9ee82d1c2e49f41771d5c00

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Citations in the corpus

BRENDA in 2015: exciting developments in its 25th year of existence (2014, methodology): “(ii) Orthology data of KEGG and annotations of PATRIC (21) were included as additional data sources.”
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential (2015, methodology): “such as isolation source of each bacterial isolate was collected from original literature, PATRIC [17] and the”
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data (2013, background): “There are many databases available containing genes encoding toxins and virulence factors along with other genes traditionally associated with pathogenicity [13,14].”
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes (2015, methodology): “It searches against custom BLAST databases that have been built from ARDB 34 and CARD 35 for finding potential antibiotic resistance genes; DrugBank 36 and TTD 37 for finding potential drug targets; VFDB 38 ,Victors 39 and the PATRIC virulence factors 10,33 for finding potential virulence factors; a”
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) (2013, background): “Data are summarized at the level of the individual genome and across taxonomic levels (21).”