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

Scott F. Saccone, Jiaxi Quan, Gaurang Mehta, Raphael Bolze, Prasanth Thomas, Ewa Deelman, Jay A. Tischfield, John P. Rice

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

Original languageEnglish
Pages (from-to)D901-D907
JournalNucleic acids research
Issue numberSUPPL. 1
StatePublished - Jan 2011


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