Building on BMI 507 as a prerequisite, this course first provides a review of the theories underlying biomedical knowledge representation and ontology. The methods and tools for applied ontology as well as the management and maintenance of biomedical ontologies will be discussed in detail, including the principles of ontological realism and the implementation thereof in the Basic Formal Ontology (BFO). Students will gain experience with the Web Ontology Language (OWL) and the limitations thereof, and with utilities to query ontologies expressed in OWL. The students will learn how to use and evaluate classifiers and their role in subsumption. They will learn both the transitive and reflexive closure of subsumption of a KR system and its applied use in ontology development, maintenance and use. This course also provides an in-depth review of current theories and research underlying the development of biomedical ontologies, a comparative critical analysis of the major current biomedical ontologies as well as the methods and tools for biomedical ontology development, use and evaluation.