The integration of a computer-based system dealing with clinical guidelines with a medical ontology can provide several advantages, including standardization and knowledge sharing. Furthermore, in order to operate in the clinical practice, guideline systems must also interact with the hospital databases to retrieve patients’ data. Unfortunately, currently there seems not to be any “standard” consensus model either for the medical ontology or for (the conceptual structure of) patient databases (even if several interesting proposals have been carried out). In this paper we show how we are extending the GLARE guideline manager in order to strictly interact with both a medical ontology and a patient Database, in such a way that GLARE is not committed to any specific ontology and database (i.e., different ontologies and/or databases can be used).