BioQuery is an application that helps scientists automate database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. The application is implemented on a portable object framework that can provide database-searching capability to other applications. This framework is easily extensible, allowing users to develop plug-ins that provide access to new databases. BioQuery thus provides end-users with a complete database searching interface and updating service, and gives developers a toolkit to provide database-searching capability to their applications.