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New tools and methods for direct programmatic access to the dbSNP relational database.

Scott F Saccone1, Jiaxi Quan, Gaurang Mehta

  • 1Department of Psychiatry, Washington University, University of Southern California, Washington University, USA. ssaccone@wustl.edu

Nucleic Acids Research
|November 2, 2010
PubMed
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This summary is machine-generated.

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Researchers created free software to install and query the dbSNP database locally. This tool aids in integrating biological information for genome-wide association studies, enhancing genetic research capabilities.

Area of Science:

  • Bioinformatics
  • Genetics
  • Database Management

Background:

  • Genome-wide association studies (GWAS) require biological context for result interpretation.
  • Public biological databases like dbSNP are crucial resources for this context.
  • Efficient programmatic access to these databases is essential for large-scale genetic research.

Purpose of the Study:

  • To develop freely available software for local installation and querying of the dbSNP database.
  • To create a system for classifying dbSNP tables to facilitate common research tasks.
  • To provide web tools for broader accessibility to database querying and documentation.

Main Methods:

  • Developed free software to download and install a local MySQL implementation of the dbSNP database.

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  • Designed a classification system for dbSNP tables based on common research tasks.
  • Created custom tables and entity-relationship diagrams to optimize task-specific queries.
  • Implemented web tools for database querying and browsing documentation.

    • Main Results:

    • A functional, free software package for local dbSNP database management is now available.
    • A structured approach to dbSNP table classification and task-oriented querying has been established.
    • Web-based tools enhance user accessibility for querying and understanding the database structure.
    • The developed resources are publicly accessible at http://cgsmd.isi.edu/dbsnpq.

    Conclusions:

    • The developed software and web tools provide essential resources for programmatic querying of biological databases.
    • These tools facilitate the integration of biological information into genome-wide association studies.
    • The project enhances the ability to conduct large-scale genetic association experiments by improving data accessibility and usability.