PATRIC March 2017 Release Features over 3600 New Genomes, and New Functionality and Data Including an Antibiotics Database, AMR Phenotype Information, a Close Genome Finder Service, HPI/PPI Data and Visualization, a Compare Region Viewer, an ID-Mapping Tool, and Enhanced Global Search.¶
PATRIC March 2017 Data and Website Release:
New Genomes
In this release, PATRIC has added 3669 new genomes, bringing the total number of genomes in PATRIC to nearly 98,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing Page. UniProt ID Mappings have also been updated.
Antibiotics Database
PATRIC now has an antibiotics database that includes information such as name, description, chemical structure, mechanism of action, and pharmacology. Information is incorporated from PubChem for approximately 100 antibiotics for which PATRIC has AMR phenotype data. Antibiotics data are displayed via a new Antibiotics Overview Page with tabs for:
Basic information / overview of the antibiotic and publications related to resistance to that antibiotic
All AMR phenotype data for a given antibiotic
Related AMR genes
Related AMR k-mer regions predicted by the classifiers
An example overview page for Amikacin can be accessed at https://www.patricbrc.org/view/Antibiotic/?eq(antibiotic_name,amikacin)#view_tab=overview
AMR Phenotype Data
PATRIC has a new “AMR phenotypes” tab at the taxon and genome levels that provides list of genomes, their AMR phenotypes, and corresponding metadata about the laboratory methods and testing standards. The table allows filtering by antibiotic and phenotype to create genome groups containing resistant and susceptible genomes for that antibiotic. An example can be accessed from https://www.patricbrc.org/view/Taxonomy/1763#view_tab=amr&filter=and(eq(antibiotic,Amikacin),eq(resistant_phenotype,Susceptible))
Predicted AMR phenotypes from classifiers are now displayed on the genome overview pages, including private user genomes annotated using the PATRIC Annotation Service.
Similar Genome Finder Service
PATRIC now has a new Close Genome Finder Service that, for a user-selected public or private genome, or for an uploaded FASTA file, will find the closest related public genomes (by sequence) in PATRIC using the MInHash algorithm to perform comparisons. The service is available from the Services menu at https://www.patricbrc.org/app/GenomeDistance.
Host-Pathogen Interaction / Protein-Protein Interaction (HPI/PPI) Data and Visualization
PATRIC now includes the latest experimental and computational HPI/PPI data from greater than 15 public repositories, including STRINGDB with a total of 55 million protein-protein interactions. There is a new Interactions tab at the Interactions genome, and gene levels, showing interactions as table and graph. Examples are accessible at https://www.patricbrc.org/view/Genome/83332.12#view_tab=interactions and https://www.patricbrc.org/view/Feature/PATRIC.83332.12.NC_000962.CDS.2507203.2507637.fwd#view_tab=interactions&filter=false
Compare Region Viewer
PATRIC has a new Compare Region Viewer that displays flanking regions of user selected genomes for a particular gene. This is a re-implementation of the original SEED Compare Region Viewer using JavaScript and PattyFams. An example is accessible at https://www.patricbrc.org/view/Feature/RefSeq.83332.12.NC_000962.CDS.2726806.2727339.fwd#view_tab=compareRegionViewer
Advanced Search Enhancements
PATRIC has enhanced the Global Search to allow users to search for “all” or “any” of the search terms and searching for exact terms. The option of “Any exact terms” is particularly useful for searching using a list of gene or genome IDs. The Global Search is available at the top right of any page in PATRIC.
ID Mapper Tool
The new PATRIC ID Mapper Tool uses UniProt ID Mapping data to allows users to enter a list of PATRIC IDs and map them to corresponding external database identifiers, or vice versa. The tool is accessible at https://www.patricbrc.org/app/IDMapper.