{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T22:31:29Z","timestamp":1778884289782,"version":"3.51.4"},"reference-count":53,"publisher":"Oxford University Press (OUP)","funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400027C"],"award-info":[{"award-number":["HHSN272201400027C"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https:\/\/www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.<\/jats:p>","DOI":"10.1093\/nar\/gkz943","type":"journal-article","created":{"date-parts":[[2019,10,12]],"date-time":"2019-10-12T19:28:51Z","timestamp":1570908531000},"source":"Crossref","is-referenced-by-count":411,"title":["The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities"],"prefix":"10.1093","author":[{"given":"James J","family":"Davis","sequence":"first","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alice R","family":"Wattam","sequence":"additional","affiliation":[{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"},{"name":"Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA\u00a022904, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramy K","family":"Aziz","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562\u00a0Cairo, Egypt"},{"name":"Center for Genome and Microbiome Research, Cairo University, 11562\u00a0Cairo, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Brettin","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL\u00a060439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralph","family":"Butler","sequence":"additional","affiliation":[{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"},{"name":"Middle Tennessee State University, Murfreesboro, TN\u00a037132, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rory M","family":"Butler","sequence":"additional","affiliation":[{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Chlenski","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL\u00a060527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neal","family":"Conrad","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Allan","family":"Dickerman","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA\u00a022904, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily M","family":"Dietrich","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL\u00a060439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph L","family":"Gabbard","sequence":"additional","affiliation":[{"name":"Virginia Tech, Blacksburg, VA\u00a024061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5472-2912","authenticated-orcid":false,"given":"Svetlana","family":"Gerdes","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL\u00a060527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Guard","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronald W","family":"Kenyon","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA\u00a022904, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dustin","family":"Machi","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, 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60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric K","family":"Nordberg","sequence":"additional","affiliation":[{"name":"Transportation Institute, Virginia Tech University, Blacksburg, VA\u00a024061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary J","family":"Olsen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Illinois, Urbana, IL\u00a061801, USA"},{"name":"Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL\u00a061801, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert D","family":"Olson","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jamie C","family":"Overbeek","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ross","family":"Overbeek","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce","family":"Parrello","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gordon D","family":"Pusch","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL\u00a060527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maulik","family":"Shukla","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"},{"name":"Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Thomas","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL\u00a060637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margo","family":"VanOeffelen","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL\u00a060527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Veronika","family":"Vonstein","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL\u00a060527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew S","family":"Warren","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA\u00a022904, 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USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rick","family":"Stevens","sequence":"additional","affiliation":[{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL\u00a060439, USA"},{"name":"University of Chicago, Department of Computer Science, Chicago, IL\u00a060637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,31]]},"reference":[{"key":"2019103104193083200_B1","doi-asserted-by":"crossref","first-page":"D401","DOI":"10.1093\/nar\/gkl858","article-title":"PATRIC: the VBI pathosystems resource integration center","volume":"35","author":"Snyder","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2019103104193083200_B2","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis 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