title: The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
abstract: BACKGROUND
  The 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.
  
  
  METHODS
  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.
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Jean-Pierre A
authors.initials: JP
authors.lastname: Kocher
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Quest
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Duffy
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Meiners
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Raymond M
authors.initials: RM
authors.lastname: Moore
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: David
authors.initials: D
authors.lastname: Rider
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Asif
authors.initials: A
authors.lastname: Hossain
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Steven N
authors.initials: SN
authors.lastname: Hart
authors.affiliation: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Department of Research IT, Mayo Clinic, Rochester, MN 55905, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.
authors.forename: Valentin
authors.initials: V
authors.lastname: Dinu
mesh_terms: D023281:Genomics; D012985:Software Design