Abstract. This paper reports our experience with OWL for the Foundational Model of Anatomy (FMA). We show that converting the FMA from Protégé into OWL DL was possible, with most features of the original FMA captured. The conversion relies on translation and enrichment rules, implemented with flexible options. Unsurprisingly, reasoning with OWL proved to be a real challenge, due to the sheer size and complexity of the FMA. As the entire FMA in OWL DL raised inference problems hard to solve in terms of time and memory, an incremental approach was adopted. A number of various smaller versions that Racer could handle were successfully tested. Some inconsistencies were identified and some classes reclassified. The analysis of the results obtained so far shows the benefits of representing the FMA in OWL and, more generally, the usefulness of DLs reasoning techniques for large-scale biomedical ontologies shared on the Web. 1

Methods for comparing associative relationships across ontologies often rely solely on lexical similarity between the names of the relationships, which may lead to missed matches and inaccurate matches. In this paper, we propose a novel method based on the analysis of paths between equivalent concepts across ontologies. Patterns of relationships are identified for each associative relationship. The most frequent patterns indicate a correspondence between an associative relationship in one ontology and one relationship (or combination thereof) in the other. We applied this method to two ontologies of anatomy. Our method was able to identify the correspondence between relationships even in the absence of lexical similarity between relationship names. The various types of matches identified are discussed as well as the application of this method to detecting inconsistencies across the ontologies.

Abstract. This paper focuses on the migration of the Foundational Model of Anatomy from its frame-based representation in Protégé to its logical representation in OWL. First, it considers specificities of the FMA in Protégé that were taken into account for the migration, and presents some conversion rules defined for migrating FMA from Protégé 2.1 to OWL DL. Then, the incremental approach currently adopted is outlined. Preliminary results are reported, exhibiting the benefits of this work both for the FMA and for description logic systems. 1.

INTRODUCTION Although various medical knowledge representation systems claim to support reasoning, there is little work done on investigating their respective reasoning capabilities. In this regard, the objective of this study is to analyze the shared characteristics and differences of multiple representations of a given domain. With the emergence of the Semantic Web, agents relying on different ontologies needed to communicate and exchange reliable information and techniques for comparing ontologies could play a central role in this process [1, 2]. Several approaches have been explored to compare ontologies, resulting in several byproducts: merging, where a new ontology is created [3, 4], transformation from one to another [5], and alignment, where a mapping is built between two ontologies [6]. In this study, alignment is the technique of choice because we do not intent to create any new system or to alter existing ones. The methods we use for aligning ontologies act not only at t