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Protein-protein interaction (PPI) databases store the whole set of protein interactions in organism. In spite of the availability of much biological information spread on different sources (e.g. Gene Ontology), neither proteins nor interactions are generally annotated in PPI databases. This results in very poor querying capabilities of PPI databases that enable very simple queries. The annotation of proteins and interactions stored in PPI databases may allow the implementation of more powerful querying interfaces. The paper presents a software architecture for the annotation of existing PPI databases with information extracted from Gene Ontology. A simple extension of the query interface of an existent PPI database is discussed.