The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- Bioinformatics
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Bioinformatics 30 (13), 1920-1922, 2014-03-10
Oxford University Press (OUP)