The Kidney Precision Medicine Project (KPMP) is a multicenter NIH-funded project designed to systematically collect and analyze clinical data, pathology images, and biosamples, including kidney biopsies, for high-throughput molecular omics phenotyping of individuals with common forms of acute kidney injury and chronic kidney disease. The integration of heterogeneous data types into a data and visual representation that is open to the public and that supports flexible search and cohort subsetting is a significant computational task. Ontologies are powerful tools for organizing different data types and creating connections between data elements through a variety of defined relationships. Given that ontologies are critical for the success of ambitious and data-intensive initiatives, the KPMP has developed the Kidney Tissue Atlas Ontology and Ontology of Precision Medicine and Investigation to organize and harmonize a large amount of heterogeneous data collected from across the consortium for analysis. In this review article, we discuss ontologies and their role in the KPMP and demonstrate how they will be used to support the creation of the Kidney Tissue Atlas and to revise existing definitions of kidney disease.