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Much of the information that exists in patient clinical reports is difficult to access, as it is often in unstructured text form. To make easy access and search, we develop a tool for extracting named entities from free French reports. A rule-based approach is applied to clinical reports corpus of infectious diseases to extract semantic content in the form of named entities and properties. Two objectives can be achieved through this work; (1) the patient data anonymization and (2) the structured database fill in dedicated for future medical applications.