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The history of data has a crucial importance almost in every scientific application. In order to trust the correctness of data, the ability to determine the origin of data becomes an important issue. Provenance information summarizes the origin of items, the history of the ownership of items and the actions performed on them. Ensuring that data is kept safe from corruption or illegal accesses and detecting privacy breaches on data should be achieved by integrating provenance concepts with security concepts. Information such as an individual’s infectious disease history is highly sensitive and should not be revealed to an unauthorized user. This historical data needs privacy. We propose a privacy-aware provenance management model by creating policies and querying provenance data to detect policy violations. We illustrate our proposed model by integrating it with infectious disease and vaccination domains.