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Ontologies have long been employed in the life sciences to formally represent and reason over domain knowledge and they are employed in almost every major biological database. Recently, ontologies are increasingly being used to provide background knowledge in similarity-based analysis and machine learning models. The methods employed to combine ontologies and machine learning are still novel and actively being developed. We provide an overview over the methods that use ontologies to computedoi:10.1093/bib/bbaa199 pmid:33049044 pmcid:PMC8293838 fatcat:3mqrjqnggrhdrkvsl6w4odazeu