Using Rules to Investigate the Differences in Partonomy between Biomedical Ontologies

In this study we constructed rules to systematically identify the differences as well as similarity in partonomy between two large biomedical ontologies. For a group of one-to-one mapped concepts, we distinguish among different types of parts defined for these mapped concepts, and the structural imbalance between two systems. As a result, 1.4% of the concept mappings have exactly the same part-whole relations, 68.4% do not have any parts, and 30.2% mappings are modeled differently, including additional parts, more detailed part paths, and different intermediate concepts in the part paths. This is a parallel study to our previous work where granularity mismatches in is-a classification among ontologies were identified. Using rules and the rule inference engine enables an automatic and scalable investigation of the structural incompatibility among biomedical ontologies.