To carry ecologically-relevant biodiversity research, one must collect chunks of information on species and their habitats from a large number of institutions and correlate them using geographic, biologic and ecological knowledge. Distribution and heterogeneity inherent to biodiversity data pose several challenges, such as how to find and merge relevant information on the Web, and process a variety of ecological and spatial predicates. This paper presents a framework that exploits advances in data interoperability and Semantic Web technologies to meet these challenges. The solution relies on ontologies and annotated repositories to support data sharing, discovery and collaborative biodiversity research. A prototype using real data has implemented part of the framework.