Abstract. This paper analyzes the requirements and presents a novel approach to the development of a system for epidemiological data collection and integration based on the principles of interoperability and modularity. Accurate and timely epidemic models require the integration of large, fresh datasets. Thus, from an e-science perspective, collected data should be shared seamlessly across multiple applications. This is addressed by our approach, MEDCollector, trough workflow design enables the extraction of data from multiple Web sources. The mapping of extracted entities to ontologies will guarantee the consistency within gathered datasets, and therefore enhance epidemic modeling tools.