Human Phenotype Ontology (HPO)

About the resource

Type of resource: Ontology
License/availability: Open source
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The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease.

A key challenge in genomics is to understand the phenotypic consequence of genomic variation. With the advent of next-generation sequencing technologies, the challenge is no longer to generate DNA sequence data, but to interpret them. The analysis of phenotypic abnormalities provides a translational bridge from genome-scale biology to a disease-centered view on human pathobiology. It is becoming clear that detailed phenotype data, combined with ever-increasing amounts of genomic data, have an enormous potential to accelerate the identification of clinically actionable complications of disease subtypes with prognostic or therapeutic implications as well as to improve our understanding of human health and disease.

The description of phenotypic variation is a central topic for all of those studies, and therefore, a systematic human and computer interpretable representation is crucial due to the complex nature of human disease. Therefore, the usage of standardized measures for capturing phenotypic abnormalities is of major importance, but in the past, it has been difficult to agree on common semantic and technical standards as well as the ethical and legal framework for collecting and analyzing human phenotype data.

An ontology provides a conceptualization of a domain of knowledge, allowing communication between researchers and makes the information readable and ‘understandable’ for computers. 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. It was initially developed using information from Online Mendelian Inheritance in Man (OMIM), which is a hugely important data resource in the field of human genetics and beyond. The HPO is organized as three independent subontologies that cover different categories; the mode of inheritance, the onset and clinical course and the largest category of phenotypic abnormalities.

Each class of the HPO has a unique and stable identifier (e.g. HP:0002145), a label and a list of synonyms. Most of the classes are accompanied by a detailed textual definition created by clinical experts. Additionally, HPO classes now contain one or more references to other resources to promote interoperability among different biomedical research areas.