Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts

We investigated the interconnection on knowledge of biological molecules, biological phenomena, and diseases to efficiently collect information regarding the functions of chemical compounds and gene products, roles, applications, and involvements in diseases using knowledge graphs (KGs) developed from Resource Description Framework (RDF) data and ontologies. NikkajiRDF linked open data provide information on approximately 3.5 million chemical compounds and 694 application examples. We integrated NikkajiRDF with Interlinking Ontology for Biological Concepts (IOBC), including approximately 80,000 concepts, information on gene products, drugs, and diseases. Using IOBC’s ontological structure, we confirmed that this integration enabled us to infer new information regarding biological and chemical functions, applications, and involvements in diseases for 5038 chemical compounds. Furthermore, we developed KGs from IOBC and added protein, biological phenomena, and disease identifiers used in major biological databases: UniProt, Gene Ontology, and MeSH to the KGs. Using the extended KGs and federated search to the DisGeNET, we discovered more than 60 chemicals and 700 gene products, involved in 32 diseases.