Biodiversity Information Systems are complex software systems that present data management solutions to allow researchers to analyze species and their interactions. The complexity of these systems varies with the data handled, users targeted and environment in which they are executed. An open problem to be faced especially in a Web environment is data heterogeneity, and the diversity of user vocabularies and needs. This hampers query processing. This paper presents a tool based on Web services to expand and process biodiversity queries using ontology information. This solution relies on a new database organization, also described here, which combines in a single model data collected in the field with data found in archival sources. This tool is being tested using real case studies, within a large Web-based biodiversity system.