The Human Phenotype Ontology in 2021

Abstract

Abstract The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

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Affiliated Institutions

• Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases AT
• Lawrence Berkeley National Laboratory US
• King Edward Memorial Hospital AU
• University of Connecticut US
• American College of Medical Genetics US
• Newcastle University GB
• Curtin University AU
• University of Luxembourg LU
• University Medical Center Freiburg DE
• CeMM Research Center for Molecular Medicine AT
• The Kids Research Institute Australia AU
• Istituti di Ricovero e Cura a Carattere Scientifico IT
• University of Pennsylvania US
• The University of Western Australia AU
• Medical University of Graz AT
• Ludwig-Maximilians-Universität München DE
• Oregon State University US
• Children's Hospital of Philadelphia US
• European Bioinformatics Institute GB
• Orphanet FR
• Inserm FR
• Istituto Giannina Gaslini IT
• Austrian Academy of Sciences AT
• William Harvey Research Institute GB
• Queen Mary University of London GB
• University of Michigan US
• University of Freiburg DE
• University of Genoa IT
• Jackson Laboratory US
• Johns Hopkins University US
• German Center for Infection Research DE
• Oregon Health & Science University US
• Ghana Health Service GH
• University of Colorado Anschutz Medical Campus US
• Newcastle upon Tyne Hospitals NHS Foundation Trust GB
• German Center for Lung Research DE
• SimulConsult US

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