Website Review: Pathosystems Resource Integration Center (PATRIC). http://www.patricbrc.org

Abstract

Tabled 1REVIEWER RATINGCoverage of relevant topics★★★★★Improvement over previously available media★★★Citations of supporting references★★★Style of presentation and formatting★★★Quality of figures★★★Interactivity★★★★★Ease of navigation★★★Overall★★★★Stars★: poor; ★★: adequate; ★★★: fair; ★★★★: good; ★★★★★: excellent. Open table in a new tab Stars ★: poor; ★★: adequate; ★★★: fair; ★★★★: good; ★★★★★: excellent. Microbiome research is among the hottest areas in the field of gastroenterology, including gastrointestinal infections and inflammatory bowel diseases. Many of the bacterial phylogenomic data are reported from numerous sources, but the data are broadly spread out, thereby increasing the difficulty of comparative analysis of those mass data sets. Pathosystems Resource Integration Center (PATRIC) is the Bacterial Bioinformatics Resource Center that is funded by the National Institutes of Allergy and Infectious Disease. PATRIC is a freely available online resource that stores and integrates a variety of data types from many bacterial pathogens as well as closely related symbiotic commensal species. For example, genomics, transcriptomics, protein–protein interaction, and 3-dimensional protein structures of bacterial pathogens and symbionts are available on the PATRIC website. Currently, >13,000 genomes are in PATRIC and they are all being annotated using Rapid Annotations Subsystem Technology. The goal of PATRIC is to provide an interface for scientists in the field of bacterial infectious diseases to search data and information, and to conduct comprehensive comparative genomic and other analyses using a single website. A specific feature of PATRIC is to provide a searchable format that integrates bacterial metabolic pathways. Bacterial metabolic pathways can be identified by searching taxonomy, enzyme commission number, pathway ID, pathway name, and/or specific annotation type. Pathways are presented in a table format, and can be further displayed as a KEGG map and a heat map when specific pathways are selected. The pathway analysis tool is a very powerful resource because it allows one to identify specific metabolic pathways associated with the growth of particular bacteria, thus advancing our understanding of the pathogenesis of infectious pathogens. However, the pathway tool is not yet optimized for comparative analyses of the metabolic pathways among different bacteria. Researchers are also able to access disease-related information through PATRIC. The disease view in PATRIC enables one to see the summarized relationship between pathogens, diseases, and associated genes both in pathogens and the host. This resource has the potential to improve our understanding of host–pathogen–disease association that is important for clarifying the mechanisms of disease as well as optimizing the diagnostic process and the development of new therapeutics. In addition, as a powerful bioinformatics tool for the analysis of existing bacterial taxonomy data, researchers can upload their own data to a workspace in PATRIC where both public and confidential data can be stored and analyzed. It is noteworthy that the private workspace on the PATRIC website is completely confidential and only accessible to authorized users. This allows the website users to control who has access to confidential mass genomic data of their targeted bacteria. Because PATRIC comprises various tools used to analyze bacterial genomic information, it requires the researchers to spend some time learning how to use the website. In this regard, PATRIC provides an excellent video as well as easy-to-read, written tutorials. The tutorials thoroughly explain how to use the complex analytical tools most effectively. Furthermore, the bacterial genomic database as well as the bioinformatics analysis tools in PATRIC keep improving and expanding, and will further provide many new capabilities for the microbial researches. Bottom Line: The PATRIC is a freely available online resource that provides powerful bacterial bioinformatics tools. The website is extremely useful to the research community involved in bacterial infectious diseases as well as the gut microbiome.