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The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin.
Afiliação
  • Kocher JP; 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.
  • Quest DJ; 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.
  • Duffy P; 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.
  • Meiners MA; 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.
  • Moore RM; 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.
  • Rider D; 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.
  • Hossain A; 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.
  • Hart SN; 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.
  • Dinu V; 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.
Bioinformatics ; 30(13): 1920-2, 2014 Jul 01.
Article em En | MEDLINE | ID: mdl-24618464
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. 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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Design de Software Idioma: En Ano de publicação: 2014 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Design de Software Idioma: En Ano de publicação: 2014 Tipo de documento: Article