<p>Medical ontologies have been a focus of constant attention in recent years as one of the fundamental techniques and knowledge bases for clinical decision support applications. In this paper, we discuss the description framework of our anatomy ontology with a focus on representing topological information, which is required for anatomical reasoning in clinical decision support applications. Our framework has major advantages over preceding studies with respect to: (1) representations of branching sequence; (2) combined representation of relevant knowledge with the use of Ògeneral structural componentÓ; and (3) cooperation with the disease and abnormality ontologies.</p>