Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient’s phenotype. The development of two new ontologies — the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation — will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine. Ontologies are powerful tools that facilitate the integration of large and disparate data sets. Here, researchers from the Kidney Precision Medicine Project provide an introduction to ontologies, including those developed by the consortium, describing how these will be used to improve the annotation of kidney-relevant data, eventually leading to new definitions of kidney disease in support of precision medicine. Key points Ontologies are powerful tools for organizing, integrating and linking heterogeneous data types, especially in the biomedical sciences. Significant additions to biomedical ontologies are necessary to better define kidney molecular and histopathological phenotypes, which is critical for kidney precision medicine. The Kidney Precision Medicine Project is creating a community-based Kidney Tissue Atlas to integrate molecular, cellular and anatomical knowledge of the kidney. The development of the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation will facilitate data collection, harmonization and analysis in support of kidney precision medicine. The Kidney Precision Medicine Project has extensively adopted, reused and extended community-based reference ontologies