PATRIC, the bacterial bioinformatics database and analysis resource

By A. Wattam, David Abraham, O. Dalay, T. Disz, T. Driscoll, Joseph L. Gabbard, Joseph J Gillespie, R. Gough, D. Hix, Ron Kenyon and 18 more. Nucleic Acids Res., 2013

1,188 citations recorded by the source corpus.

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.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/10b40befe5942e997f88ab40bac1acd931147893

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Citations in the corpus

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes (2015, methodology): “…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; and the human reference genome sequence 40 for finding potential human homologs, which is an important…”
JBrowse: a dynamic web platform for genome visualization and analysis (2016, background): “Sites that use JBrowse (or JBrowse-based tools) span plant genomics [19–25], animal genomics [12, 26–29], and disease-related databases [30–34].”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “Other databases such as the DOE’s Joint Genome Institute Integrated Microbial Genomes & Microbiomes (JGI IMG/M) database (7), the PATRIC (Pathosystems Resource Integration Center) database (8) and Ensembl Bacteria (9) provide additional layers of information for the deposited genomes through integra”
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography (2016, methodology): “profiling reveals novel patterns of bacterial transmission and biogeography”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “PATRIC has made significant improvements since it was last described in Nucleic Acids Research (NAR) (1).”