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We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.doi:10.1093/bioinformatics/bty259 pmid:29949999 pmcid:PMC6022543 fatcat:nmb7uxfcgzhpvix3ccczi3hlge