Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

By A. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, T. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, T. Disz, Joseph L. Gabbard and 18 more. Nucleic Acids Res., 2016

1,522 citations recorded by the source corpus.

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.

Subfields: Clinical Biochemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0ff76dd78e47f4534ee148b644f1f2707bc70df5

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Citations in the corpus

• Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT (2019, neutral): “To manually assess the 28 MAGs whose classification was inconsistent with the published classifications, we created a phylogenomic tree of those bins together with closely related genomes that were downloaded from PATRIC [40] on January 16, 2018.”
• VFDB 2019: a comparative pathogenomic platform with an interactive web interface (2018, background): “Several other online resources for bacterial genomic analysis also provide VF screening services, such as PATRIC (19), VRprofile (20) and VirulenceFinder (21).”
• The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “Since last described in Nucleic Acids Research in 2016 (3), PATRIC has undergone a series of updates and improvements.”
• BRENDA, the ELIXIR core data resource in 2021: new developments and updates (2020, methodology): “For bacteria and archaea the annotation data from PATRIC (32) are also integrated.”
• MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data (2017, methodology): “The 105 strain sets were obtained mainly from the Genomes Online Database (GOLD) database (29) and the Pathosystems Resource Integration Center (PATRIC) (30), organized primarily based on their phenotypic traits.”