NLM anatomical ontology alignment system: Results of the 2006 ontology alignment contest

Abstract. An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with and reasoning across these ontologies. The objective of this paper is to present our experience in aligning two large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The anatomical ontologies under investigation are the Foundational Model of Anatomy (FMA) and GALEN. Our approach to aligning concepts is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). Overall, the lexical alignment followed by structural validation identified 3,029 pairs of equivalent concepts in the FMA and GALEN, accounting for about 4 % of all FMA concepts and 32 % of all GALEN concepts