Curation, integration and visualization of bacterial virulence factors in PATRIC

Bioinformatics. 2015 Jan 15;31(2):252-8. doi: 10.1093/bioinformatics/btu631. Epub 2014 Sep 30.


Motivation: We've developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity.

Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A-C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein-protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC.

Availability and implementation: All tools and data are freely available at PATRIC (

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / pathogenicity
  • Bacterial Infections / microbiology*
  • Bacterial Proteins / metabolism*
  • Computer Graphics*
  • Databases, Factual*
  • Gene Expression Profiling
  • Genome, Bacterial
  • Genomics
  • Humans
  • Protein Interaction Mapping
  • Systems Integration
  • Virulence / genetics*
  • Virulence Factors / metabolism*


  • Bacterial Proteins
  • Virulence Factors