PATRIC

PATRIC[1] (Pathosystems Resource Integration Center) is a bacterial bioinformatic website from the Bioinformatics Resource Center. It is an information system integrating databases with various types of data about bacterial pathogens (transcriptomic, proteomic, structure, biochemical) together with analysis tools. Freely available, it is designed to support the biomedical research community's work on bacterial infectious diseases via these integrations of various pieces of pathogen information.

For other uses, see Patric (disambiguation).

Description

PATRIC, is a project of Virginia Tech's Cyberinfrastructure Division, and is funded by the National Institutes of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH). PATRIC centralize available bacterial phylogenomic data, proteomic and other various experiment pieces of data linked to specific pathogens from numerous sources.[2] Its goal specifically for the bacterial research community, in order to save biologists time and effort when conducting comparative analyses. The PATRIC platform provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses in a one-stop shop.

  • Consistent annotations across all sequenced bacterial species from GenBank.
  • Annotate your bacterial genome for free in less than 24 hours using the same RAST annotation service that is used at PATRIC.
  • Data and Information Searches
  • Perform a PATRIC global search or conduct advanced searches based on Taxonomy, Gene Name, Locus Tag, Protein Function/Families, Pathways, EC Numbers, GO Terms, Host-Pathogen Interactions, and more.
  • Perform a BLAST search against plasmid-specific BLAST databases containing genomic sequences or proteins in PATRIC.
  • Perform enhanced literature search and text mining techniques to identify genes, proteins, diseases, drugs, organisms, and other entities of interest.
  • Personal workspace that allows users to permanently save sequences of interest collected from PATRIC. From here manage and analyze saved data within your customized groups.
  • Numerous comparative analysis and interactive visualizations to help investigators discover emergent properties in complex systems. Exportable sequences and other specifics about the data used to create your custom visualizations.
  • Rich, interactive visualizations that support analyses such as, a bird's-eye view of the conservation (or lack thereof) of particular genes of interest, discerning how many proteins have the same function within a single genome, and identifying proteins with multiple homologs or paralogs across a set of genomes.
  • Freely available data and analysis results, presented in tabular, graphic, and downloadable formats.

Bacterial Organisms Covered in the PATRIC Database

    About Cyberinfrastructure Division and VBI

    The CyberInfrastructure Division at VBI develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research and other research fields. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. CyberInfrastructure Division has developed many public resources for curated, diverse molecular and literature data from various infectious disease systems, and implemented the processes, systems, and databases required to support them. It also conducts research by applying its methods and data to make new discoveries of its own.

    The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today's key challenges in the biomedical, environmental, and plant sciences.

    See also

    References
    1. Gillespie JJ, Wattam AR, Cammer SA, et al. (November 2011). "PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species". Infection and Immunity. 79 (11): 4286–98. doi:10.1128/IAI.00207-11. PMC 3257917. PMID 21896772.
    2. Sobral B, Chunhong Mao, Maulik Shukla, Dan Sullivan, Chengdong Zhang (3 January 2013). "Informatics-Driven Infectious Disease Research". In Fred A, Gamboa H, Filipe J (eds.). Biomedical Engineering Systems and Technologies. Springer Berlin. pp. 3–11. ISBN 9783642297526. Retrieved 5 March 2022.{{cite book}}: CS1 maint: date and year (link)
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