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Conducting bioinformatic analyses involves biologists in expressing requests over a range of highly heterogeneous information sources and software tools. Such activities are laborious, and require detailed knowledge of the data structures and call interfaces of the different sources. The TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) project seeks to make the diversity in data structures, call interfaces and locations of bioinformatics sources transparent to users. In TAMBIS, queries are expressed in terms of an ontology implemented using a description logic, and queries over the ontology are rewritten to a middleware level for execution over the diverse sources. This paper describes query processing in TAMBIS, focusing in particular on the way source-independent concepts in the ontology are related to source-dependent middleware calls, and describing how the planner identifies efficient ways of evaluating user queries.