{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T08:28:28Z","timestamp":1778920108383,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,12,28]],"date-time":"2016-12-28T00:00:00Z","timestamp":1482883200000},"content-version":"vor","delay-in-days":1024,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u2003The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines.<\/jats:p>\n               <jats:p>Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http:\/\/bioinformaticstools.mayo.edu .<\/jats:p>\n               <jats:p>Contact: \u00a0Kocher.JeanPierre@mayo.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu137","type":"journal-article","created":{"date-parts":[[2014,3,12]],"date-time":"2014-03-12T00:16:49Z","timestamp":1394583409000},"page":"1920-1922","source":"Crossref","is-referenced-by-count":74,"title":["The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation"],"prefix":"10.1093","volume":"30","author":[{"given":"Jean-Pierre A.","family":"Kocher","sequence":"first","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and 3 Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel J.","family":"Quest","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and 3 Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Duffy","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and 3 Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael A.","family":"Meiners","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and 3 Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raymond M.","family":"Moore","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and 3 Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Rider","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and 2 Department of Research IT, Mayo 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