We present the design and implementation of VISAGE (VISual AGgregator and Explorer), a query interface for clinical research. We follow a user-centered development approach and incorporate visual, ontological, searchable and explorative features in three interrelated components: Query Builder, Query Manager and Query Explorer. The Query Explorer provides novel on-line data mining capabilities for purposes such as hypothesis generation or cohort identification. The VISAGE query interface has been implemented as a significant component of Physio-MIMI, an NCRR-funded, multi-CTSA-site pilot project. Preliminary evaluation results show that VISAGE is more efficient for query construction than the i2b2 web-client.