  The ever-increasing amount of data in biomedical research, and in cancer
research in particular, needs to be managed to support efficient data access,
exchange and integration. Existing software infrastructures, such caGrid,
support access to distributed information annotated with a domain ontology.
However, caGrid's current querying functionality depends on the structure of
individual data resources without exploiting the semantic annotations. In this
paper, we present the design and development of an ontology-based querying
functionality that consists of: the generation of OWL2 ontologies from the
underlying data resources metadata and a query rewriting and translation
process based on reasoning, which converts a query at the domain ontology level
into queries at the software infrastructure level. We present a detailed
analysis of our approach as well as an extensive performance evaluation. While
the implementation and evaluation was performed for the caGrid infrastructure,
the approach could be applicable to other model and metadata-driven
environments for data sharing.
