The annotation practice is an almost daily activity used by healthcare professionals (PHC) to analyze patients' records, collaborate, share knowledge, and communicate. These annotations are generated within a healthcare cycle. Similarly, this cycle represents the life cycle of annotations in the patient record. The exponential increase in the number of medical annotation systems made the choice of a system by a PHC difficult, in a well-defined context (biology, radiology) and according to his/her needs to the functionalities offered by these tools. Therefore, the authors propose two taxonomies to distinguish annotation tools developed by industry and academia over the last two decades. The first classification provides an external vision based on five generic criteria. The second classification is an internal vision that gives us an idea about the functionalities offered by these systems. Finally, these unified and integrated classifications criteria are used to organize and observe the limitation of 50 medical annotation tool systems.