In a previous work we proposed a categorial structure for the representation of adverse drug reactions consisting of 16 semantic categories and 20 relations. We present an implementation of this categorial structure in Protégé based on four WHO-ART system organ classes: Gastro-intestinal system disorders, Liver and biliary system disorders, Central & peripheric nervous system disorders, and Psychiatric disorders. We compared classification according to anatomy using SNOMED CT within the PharmARTS tool and the FMA with the Pellet reasoner. This ontology contains 210 concepts for Gastroenterology, 66 concepts for Psychiatry and 85 concepts for Neurology. Classification of disorders located in the upper gastro intestinal tract was similar using both SNOMED CT and the FMA. This work is a first step towards the comparison of two models of anatomy within a common ontology of adverse drug reactions.