Optimizing biomedical ontology alignment in lexical vector space

Biomedical ontology matching dedicates to find two heterogeneous ontologies’ alignment and address their heterogeneity problem. Typically, a biomedical ontology has various biomedical concepts that are described with various labels and datatype property names, which forms a lexical space where each label or datatype property represents one dimension. Therefore, it is an effective way to present two biomedical concepts in a vector space, and use the cosine distance to measure their similarity. In this work, we present two biomedical concepts in a lexical vector space which is constructed with their inner and context concepts’ lexical information, and then utilize two vector’s cosine distance to measure similarity value. Then, we propose a compact Evolutionary Algorithm (cEA) to find the concept correspondences. The experiment uses Ontology Alignment Evaluation Initiative (OAEI)’s testing cases, and the expeirmental results with Vector space Based Ontology Matcher (VBOM), Genetic Algorithm based Ontology Matcher (GAOM) and OAEI’s participants show the effectiveness of our proposal.