The digital transformation of companies has led to the evolution of databases towards Big Data. Our work is part of this context and concerns more particularly the mechanisms to extract datasets stored in a Data Lake and to store the data in a Data Warehouse. The latter will allow, in a second time, decisional analysis. In this paper, we present the extraction mechanism limited to relational databases. To automate this process, we used the Model Driven Architecture (MDA), which offers a formalized environment for schema transformation. From the physical schemas describing a Data Lake, we propose transformation rules that allow the creation of a Data Warehouse stored on a document-oriented NoSQL system. An experimentation of the transformation process has been performed on a medical application.