Biological knowledge is widely represented in the form of ontology-based annotations: ontologies describe the phenomena assumed to exist within a domain, and the annotations associate a (kind of) biological entity with a set of phenomena within the domain. The structure and information contained in ontologies and their annotations make them valuable for developing machine learning, data analysis and knowledge extraction algorithms, notably, semantic similarity is widely used to identify relations between biological entities, and ontology-based annotations are frequently used as features in machine learning applications.