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Database Commons - PATRIC

PATRIC

Citations: 279

z-index 30.69

Short name PATRIC
Full name Pathosystems Resource Integration Center
Description PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools.
URL https://www.patricbrc.org/
Year founded 2013
Last update & version 2017-01-31    v3.2.76
Availability Free to all users
University/Institution hosted University of Chicago
Address 5801 South Ellis Avenue Chicago, Illinois 60637-5418
City Chicago
Province/State Illinois
Country/Region United States
Contact name Ron Kenyon
Contact email help@patricbrc.org
Data type(s)
Major organism(s)
Keyword(s)
  • protein familiy
  • sequence typing data
  • three-dimensional protein structure
Publication(s)
  • Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. [PMID: 27899627]

    Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M Dietrich, Terry Disz, Joseph L Gabbard, Svetlana Gerdes, Christopher S Henry, Ronald W Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Gary J Olsen, Daniel E Murphy-Olson, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L Stevens
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  • PATRIC, the bacterial bioinformatics database and analysis resource. [PMID: 24225323]

    Alice R Wattam, David Abraham, Oral Dalay, Terry L Disz, Timothy Driscoll, Joseph L Gabbard, Joseph J Gillespie, Roger Gough, Deborah Hix, Ronald Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Robert Olson, Ross Overbeek, Gordon D Pusch, Maulik Shukla, Julie Schulman, Rick L Stevens, Daniel E Sullivan, Veronika Vonstein, Andrew Warren, Rebecca Will, Meredith J C Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W Sobral
    Nucleic acids research 2014:42(Database issue)
    279 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

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200 OK2016-01-29
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200 OK2016-01-20
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200 OK2016-01-15
200 OK2016-01-13
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200 OK2016-01-10
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Tags

Disease
Bacteria
protein familiy sequence typing data three-dimensional protein structure

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2017-06-21]
    • Shixiang Sun [2017-02-16]
    • Shixiang Sun [2016-03-25]
    • Shixiang Sun [2016-03-24]
    • Shixiang Sun [2015-11-19]
    • Shixiang Sun [2015-06-26]
Stats