Matching Biomedical Ontologies with Long Short-Term Memory Networks

Abstract

Semantic Web (SW) has attracted the increasing attention of researchers, which facilitates people to link and handle various data. Ontology is the kernel technique of SW, and biomedical ontology is a state-of-art biomedical knowledge modeling technique, which formally defines the biomedical concepts and their relationships. However, the same biomedical concepts in different biomedical ontologies could be defined in various contexts or with different terms, which yields the biomedical ontology heterogeneity problem. It is crucial to find mapping among heterogeneity concepts of different biomedical ontologies for bridging the semantic gaps, which is the so-called biomedical ontology matching. Biomedical ontology matching problem is an open challenge due to the rich semantic meaning and the flexible representation on a biomedical concept. To address this challenging problem, in this work, it is regarded as a binary classification problem, and a Long Short-Term Memory Networks (LSTM)-based ontology matching technique is proposed to solve it. Our proposal improves the quality of the alignment by introducing the char-embedding technique, which takes into account the semantic and context information of concepts. The comparing results with OAEI’s participants show the effectiveness of our proposal.