Human Phenotype Ontology > Human Phenotype Ontology Website
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An ontology is a computational representation of a domain of knowledgebased upon a controlled, standardized vocabulary for describing entities and the semantic relationships between them. The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Terms in the HPO describes a phenotypic abnormality, such as atrial septal defect.
The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. All data is available for download or can be browsed online (please see this publication first)
The HPO is now being developed in collaboration with members of the OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including the FMA, UBERONGO, ChEBI, and MPATH. The HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things. There exists a webpage for every HPO-term.
The HPO project encourages input from the medical and genetics community with regards to the ontology itself and to clinical annotations.

Monarch Initiative

Model organisms are a cornerstone of biomedical research to investigate biological processes, test gene-based disease hypotheses, and develop and test disease treatments. The HPO team is a member of the Monarch Initiative, which is developing computational and semantic resources and software to allow cross-species phenotype analysis, and to integrate information from multiple organisms including phenotypic similarity, network analysis, gene expression and function, and genomics. One such tool for using phenotypic similarity between human disease and mouse models of disease is the Exomiser.


PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders. Phenotips was developed by the group of Michael Brudno at the University of Toronto with input from the HPO team, the Monarach initiative, and the NIH Undiagnosed Diseases Program, and allows phenotypic features of patients to be encoded using HPO terms, but also allows clinicians or researchers to collect information on demographics, medical history, family history, physical and laboratory measurements, physical findings, and free-form notes.

Suggestions and Corrections

Suggestions about HPO terms, definitions, or annotations can be sent to the HPO tracker.