In recent years, the need to use NoSQL systems to store and exploit big data has been steadily increasing. Most of these systems are characterized by the property “schema less” which means absence of the data model when creating a database. This property offers an undeniable flexibility allowing the user to add new data without making any changes on the data model. However, the lack of an explicit data model makes it difficult to express queries on the database. Therefore, users (developers and decision-makers) still need the database data model to know how data are stored and related, and then to write their queries. In previous works, we have proposed a process to extract the physical model of a document-oriented NoSQL database. In this paper, we aim to extend this work to achieve a reverse engineering of NoSQL databases in order to provide an element of semantic knowledge close to human understanding. The reverse engineering process is ensured by a set of transformation algorithms. We provide experiments of our approach using a case study taken from the medical field.