An effective method of large scale ontology matching

Abstract

Background: We are currently facing a proliferation of heterogeneous biomedical data sources accessible through various knowledge-based applications. These data are annotated by increasingly extensive and widely disseminated knowledge organisation systems ranging from simple terminologies and structured vocabularies to formal ontologies. In order to solve the interoperability issue, which arises due to the heterogeneity of these ontologies, an alignment task is usually performed. However, while significant effort has been made to provide tools that automatically align small ontologies containing hundreds or thousands of entities, little attention has been paid to the matching of large sized ontologies in the life sciences domain. Results: We have designed and implemented ServOMap, an effective method for large scale ontology matching. It is a fast and efficient high precision system able to perform matching of input ontologies containing hundreds of thousands of entities. The system, which was included in the 2012 and 2013 editions of the Ontology Alignment Evaluation Initiative campaign, performed very well. It was ranked among the top systems for the large ontologies matching. Conclusions: We proposed an approach for large scale ontology matching relying on Information Retrieval (IR) techniques and the combination of lexical and machine learning contextual similarity computing for the generation of candidate mappings. It is particularly adapted to the life sciences domain as many of the ontologies in this domain benefit from synonym terms taken from the Unified Medical Language System and that can be used by our IR strategy. The ServOMap system we implemented is able to deal with hundreds of thousands entities with an efficient computation time.