Information retrieval from distributed heterogeneous data sources remains a challenging issue. As the number of data sources increases more intelligent retrieval techniques, focusing on information content and semantics, are required. Currently ontologies are being widely used for managing semantic knowledge, especially in the field of bioinformatics. In this paper we describe an ontology assisted system that allows users to query distributed heterogeneous data sources by hiding details like location, information structure, access pattern and semantic structure of the data. Our goal is to provide an integrated view on biomedical information sources for the Health-e-Child project with the aim to overcome the lack of sufficient semantic-based reformulation techniques for querying distributed data sources. In particular, this paper examines the problem of query reformulation across biomedical data sources, based on merged ontologies and the underlying heterogeneous descriptions of the respective data sources.