We describe a service-oriented approach to model, design, and implement biological processes and data. In particular, we summarize a novel service query framework to query bioinformatics services. Our approach treats biological data and computational tools as Web services. The query framework is part of an all-encompassing system that manages the end-to-end life-cycle of services, called Web Service Management System. The proposed service query framework allows users to efficiently conduct bioinformatics experiments through service queries. We describe a real life implementation of the proposed framework and our experience in its deployment.