We present the method developed for migrating the Foundational Model of Anatomy (FMA) from its representation with frames in Protégé to its logical representation in OWL and our experience in reasoning with it. Despite the extensive use of metaclasses in Protégé, it proved possible to convert the FMA from Protégé into OWL DL, while capturing most of its original features. The conversion relies on a set of translation and enrichment rules implemented with flexible options. Unsurprisingly, reasoning with the FMA in OWL proved to be a real challenge, due to its sheer size and complexity, and raised significant inference problems in terms of time and memory requirements. However, various smaller versions have been successfully handled by Racer. Some inconsistencies were identified and several classes reclassified. The results obtained so far show the advantage of OWL DL over frames and, more generally, the usefulness of DLs reasoners for building and maintaining the large-scale biomedical ontologies of the future Semantic Web.
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.
The objective of this study is to compare description logics (DLs) and frames for representing large-scale biomedical ontologies and reasoning with them. The ontology under investigation is the Foundational Model of Anatomy (FMA). We converted it from its frame-based representation in Protégé into OWL DL. The OWL reasoner Racer helped identify unsatisfiable classes in the FMA. Support for consistency checking is clearly an advantage of using DLs rather than frames. The interest of reclassification was limited, due to the difficulty of defining necessary and sufficient conditions for anatomical entities. The sheer size and complexity of the FMA was also an issue.
OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively informal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semantic Web reasoners can be used to efficiently reason with OBO ontologies. Furthermore, we show that grounding the OBO language in formal semantics is useful for the ontology development process: using an OWL reasoner, we detected a likely modeling error in one OBO ontology.
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