BiOnt is a system to perform relation extraction using a deep learning system. BiOnt, employs four types of biomedical ontologies, namely, the Gene Ontology, the Human Phenotype Ontology, the Human Disease Ontology, and the Chemical Entities of Biological Interest, regarding gene-products, phenotypes, diseases, and chemical compounds, respectively. The BiOnt system can be used to effectively populate knowledge bases regarding gold standard relations. Ultimately, it can be used to explore new experimental hypotheses providing evidence to researchers and clinicians about possible unknown associations between biomedical entities.