The Human Phenotype Ontology in 2021

Area of Science:

• Biomedical Informatics
• Genetics and Genomics
• Clinical Medicine

Background:

• The Human Phenotype Ontology (HPO) provides a standardized vocabulary for describing phenotypic abnormalities in human disease.
• Established in 2008, HPO has become a global standard for phenotype data exchange, driven by contributions from clinical experts and researchers.
• Continuous development is essential to maintain HPO's relevance and utility in a rapidly evolving scientific landscape.

Purpose of the Study:

• To report recent major extensions and enhancements to the Human Phenotype Ontology (HPO).
• To detail efforts in harmonizing computational definitions across HPO and animal model ontologies.
• To summarize advances in HPO's application in electronic health record systems and translation initiatives.

Main Methods:

• Incorporation of clinical expert guidelines, such as the International League Against Epilepsy (ILAE) guidelines, into specific HPO subontologies (e.g., seizures).
• Development of computational strategies to harmonize phenotype definitions across different ontologies for improved cross-species matching.
• Implementation and evaluation of HPO in electronic health record systems and translation into indigenous languages.

Main Results:

• Significant extensions of HPO in key areas including neurology, nephrology, immunology, pulmonology, and newborn screening.
• Demonstrated clinical validity of enhanced HPO subontologies, exemplified by the seizure subontology aligning with ILAE guidelines.
• Improved accuracy and scope of cross-species phenotype matching through ontology harmonization, benefiting tools like Exomiser.
• Progress in translating HPO into indigenous languages and its successful integration into electronic health record systems.

Conclusions:

• The Human Phenotype Ontology continues to evolve as a critical resource for standardizing and analyzing phenotypic data in human disease.
• Recent extensions and harmonization efforts enhance HPO's utility for clinical research, cross-species comparisons, and clinical applications.
• The ongoing integration of HPO into electronic health records and global translation efforts underscore its expanding impact on biomedical research and healthcare.