Nowadays, there is a growing need to collect and analyze data from different databases. Our work is part of a medical application that must allow health professionals to analyze complex data for decision making. We propose mechanisms to extract data from a data lake and store them in a NoSQL data warehouse. This will allow us to perform, in a second time, decisional analysis facilitated by the features offered by NoSQL systems (richness of data structures, query language, access performances). In this paper, we present a process to ingest data from a Data Lake into a warehouse. The ingestion consists in (1) transferring NoSQL DBs extracted from the Data Lake into a single NoSQL DB (the warehouse), (2) merging so-called "similar" classes, and (3) converting the links into references between objects. An experiment has been performed for a medical application.