A computational system based on ontologies to automate the mapping process of medical reports into structured databases.

•A computational system was developed according to software engineering prototyping.•An original ontology-based Medical Report Mapping Process was automated in this work.•The system supports automatic mapping of unstructured texts into structured format.•An experimental evaluation was performed in a set of 100 artificial textual reports.•Experts found that the system is valuable to extract and analyze textual patterns.