This article tries to formalize the process of semantically annotating a text with respect to an ontology. The semantic annotation puts fragments of a text in correspondence with the elements of an ontology, but all the difficulties consist in identifying fragments to be annotated and labels to be associated with them. We propose in this paper to extend ontologies by semantic annotation rules instead of by additional meta-lexical properties. This solution allows reusing best NLP tools which produce linguistic annotations at each of their levels. It also has the merit to distinguish clearly the process of linguistic analysis and the ontological interpretation.