In order to take advantage of the huge amount of information available on the Web and in document databases, it is necessary to design efficient techniques for retrieving, extracting and querying documents. Ontologies are playing an increasing role in these tasks, especially for content-based annotation and manipulation of documents. The objective of the ESCRIRE project is to use an ontology to annotate a set of abstracts of biological documents extracted from the NIH Medline public database, and then to query the annotated documents within a knowledge representation (KR) formalism. In this paper, we restrict our attention to the use of a description logic, namely the RACER system, within the ESCRIRE project.