Background: Unstructured health documents (e.g. discharge summaries) represent an important and unavoidable source of information.

Methods: A semantic annotator identified all the concepts present in the health documents from the clinical data warehouse of the Rouen University Hospital.

Results: 2,087,784,055 annotations were generated from a corpus of about 11.9 million documents with an average of 175 annotations per document. SNOMED CT, NCIt and MeSH were the top 3 terminologies that reported the most annotation.

Discussion: As expected, the most general terminologies with the most translated concepts were those with the most concepts identified.