The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation

  • Jean-Pierre A. Kocher
    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
  • Daniel J. Quest
    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
  • Patrick Duffy
    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
  • Michael A. Meiners
    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
  • Raymond M. Moore
    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
  • David Rider
    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
  • Asif Hossain
    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
  • Steven N. Hart
    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
  • Valentin Dinu
    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

抄録

<jats:title>Abstract</jats:title> <jats:p>Motivation:  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.</jats:p> <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> <jats:p>Contact:  Kocher.JeanPierre@mayo.edu</jats:p> <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>

収録刊行物

  • Bioinformatics

    Bioinformatics 30 (13), 1920-1922, 2014-03-10

    Oxford University Press (OUP)

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