PATRIC, the bacterial bioinformatics database and analysis resource.
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.
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60637, USA, Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60637, USA and Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de L'innovation, Lausanne, Switzerland.
Alice R
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Wattam
David
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Abraham
Oral
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Dalay
Terry L
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Timothy
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Driscoll
Joseph L
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Gabbard
Joseph J
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Gillespie
Roger
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Gough
Deborah
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Hix
Ronald
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Kenyon
Dustin
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Machi
Chunhong
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Mao
Eric K
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Nordberg
Robert
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Olson
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Overbeek
Gordon D
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Maulik
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Shukla
Julie
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Schulman
Rick L
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Daniel E
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Sullivan
Veronika
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Vonstein
Andrew
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Warren
Rebecca
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Meredith J C
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Wilson
Hyun Seung
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Yoo
Chengdong
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Zhang
Yan
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Bruno W
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Sobral
D001419:Bacteria / Q000145:classification / Q000235:genetics; D001424:Bacterial Infections / Q000382:microbiology; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D015373:Bacterial Typing Techniques; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D020407:Internet; D011487:Protein Conformation; D025941:Protein Interaction Mapping
D001426:Bacterial Proteins