In this paper, we propose a novel query-oriented, mediator-based biological data querying tool, SNPMiner. The system searches and queries Single Nucleotide Polymorphisms (SNPs) data from eight widely used web accessible databases. The system provides a domain-specific search utility, which can access and collect data from the deep web. This is a web-based system, so any user can use the system by accessing our server from their own computers. The system includes three important components, which are the web server interface, the dynamic query planner, and the web page parser. The web server interface can provide end users a unified and friendly interface. The dynamic query planner can automatically schedule an efficient query order on all available databases according to user's query request. The web page parser analyzes the layout of HTML files and extracts desired data from those files. The final results of the query are organized in a tabular format, which can be reviewed by a biological researcher.