The Foundational Model of Anatomy in OWL 2 and its use

Abstract

Objective: The objective is to represent the Foundational Model of Anatomy (FMA) in the OWL 2 Web Ontology Language (informally OWL 2), and to use it in a European cross-lingual portal of health terminologies for indexing and searching Web resources. Formalizing the FMA in OWL 2 is essential for semantic interoperability, to improve its design, and to ensure its reliability and correctness, which is particularly important for medical applications.

Method and material: The native FMA was implemented in frames and stored in a MySQL database backend. The main strength of the method is to leverage OWL 2 expressiveness and to rely on the naming conventions of the FMA, to make explicit some implicit semantics, while improving its ontological model and fixing some errors. Doing so, the semantics (meaning) of the formal definitions and axioms are anatomically correct. A flexible tool enables the generation of a new version in OWL 2 at each Protégé FMA update. While it creates by default a 'standard' version of the FMA in OWL 2 (FMA-OWL), many options allow for producing other variants customized to users' applications. Once formalized in OWL 2, it was possible to use an inference engine to check the ontology and detect inconsistencies. Next, the FMA-OWL was used to derive a lightweight FMA terminology for a European cross-lingual portal of terminologies/ontologies for indexing and searching resources. The transformation is mainly based on a reification process.

Result: Complete representations of the entire FMA in OWL 1 or OWL 2 are now available. The formalization tool is flexible and easy to use, making it possible to obtain an OWL 2 version for all existing public FMA. A number of errors were detected in the native FMA and several patterns of recurrent errors were identified in the original FMA. This shows how the underlying OWL 2 ontology is essential to ensure that the lightweight derived terminology is reliable. The FMA OWL 2 ontology has been applied to derive an anatomy terminology that is used in a European cross-lingual portal of health terminologies. This portal is daily used by librarians to index Web health resources. In August 2011, 6481 out of 81,450 health resources of CISMeF catalog (http://www.chu-rouen.fr/cismef/--accessed 29.08.12) (7.96%) were indexed with at least one FMA entity.

Conclusion: The FMA is a central terminology used to index and search Web resources. To the best of our knowledge, neither a complete representation of the entire FMA in OWL 2, nor an anatomy terminology available in a cross-lingual portal, has been developed to date. The method designed to represent the FMA ontology in OWL 2 presented in this article is general and may be extended to other ontologies. Using a formal ontology for quality assurance and deriving a lightweight terminology for biomedical applications is a general and promising strategy.