Dr. Haendel’s vision is to weave together healthcare systems, basic science research, and patient generated data through development of data integration technologies and innovative data capture strategies. The Monarch Initiative is an international consortium dedicated to integrating human and organismal genotype-phenotype data and the development of deep phenotyping techniques. This talk will focus on the use of ontologies to support knowledge and data integration across disciplinary boundaries. Strategies for how to reconcile different terminologies and examples of harmonized semantic structures for anatomy, phenotype, and disease will be discussed. Finally, we will discuss the use of these ontological resources to populate graph structures and their use to aid mechanism discovery and rare disease diagnosis.