{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T11:42:21Z","timestamp":1780486941255,"version":"3.54.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":765,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We\u2019ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org ) 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.<\/jats:p>\n               <jats:p>Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A\u2013C 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\u2013protein 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.<\/jats:p>\n               <jats:p>Availability and implementation: All tools and data are freely available at PATRIC ( http:\/\/patricbrc.org ).<\/jats:p>\n               <jats:p>Contact: \u00a0cmao@vbi.vt.edu .<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu631","type":"journal-article","created":{"date-parts":[[2014,10,2]],"date-time":"2014-10-02T06:07:10Z","timestamp":1412230030000},"page":"252-258","source":"Crossref","is-referenced-by-count":82,"title":["Curation, integration and visualization of bacterial virulence factors in PATRIC"],"prefix":"10.1093","volume":"31","author":[{"given":"Chunhong","family":"Mao","sequence":"first","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Abraham","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice R.","family":"Wattam","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meredith J.C.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maulik","family":"Shukla","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun Seung","family":"Yoo","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno W.","family":"Sobral","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,9,30]]},"reference":[{"key":"2023020116153393300_btu631-B1","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.2166\/wh.2009.036","article-title":"Virulence factors and their mechanisms of action: the view from a damage-response framework","volume":"7","author":"Casadevall","year":"2009","journal-title":"J. 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