Curated Virulence Factors¶
PATRIC Virulence Factors (PATRIC_VF)¶
PATRIC_VF is a manually curated virulence factor database, which contains the genes identified as playing a role in virulence in certain organisms. Each PATRIC_VF gene is linked to one or more journal articles that establish its virulence based on experimental evidence.
PATRIC_VF Curation Process¶
PubMed searches using the genus name and the term “virulence” were used as a first pass to identify genes that were associated with the virulence of the organism. Papers were examined, and if they provided direct evidence of the gene’s importance in virulence, the PubMed ID and the gene, genome and host names were collected from the article as well as sentences that identified the role the gene had in virulence. In addition, curators assigned a “Virulence Factor Category” from an internally derived nomenclature.
Once this information is collected, a search of the PATRIC database is initiated to find the genome that matches the one described in the article. If the same genome is located, there is a search for the gene described in the paper. If both match, there is a direct link between the published source and the gene. If the gene cannot be found, it’s not assigned to PATRIC_VF. If the genome is not found, a search is initiated for the same gene in a different genome. If this is identified, and indirect link is established between the gene and the published article. This is indicated by the source genome and the PATRIC genome having different strain names.