We propose an end-user oriented approach to querying repositories of data and provenance in e-Science environments. The approach is based on ontology models describing multiple domains ? in silico experiments, provenance, data, and applications. Those ontologies, integrated in a unified model and containing mappings to underlying data models, allow to query repositories of data and provenance in a unified way, or even combine provenance and data aspects in one query. We demonstrate QUery TRanslation tools (QUaTRo), built on top of the ontology models, which allow to construct complex queries over both data and provenance repositories, expressed in the terms of the domain familiar to end users. We present, in the context of the ViroLab virtual laboratory for infectious diseases, examples of construction of complex queries, combining provenance and data model aspects, which can be of practical value to scientists or medical users. Keywords: ontology models, end-user oriented database querying, provenance, semantic grid