HPO — Human Phenotype Ontology
Overview
The Human Phenotype Ontology is a controlled vocabulary for describing human disease phenotypes in a machine-readable, hierarchically organised format, developed primarily by The Jackson Laboratory and the Monarch Initiative. With over 18,000 terms as of 2024 covering all organ systems, it is widely used in rare disease genomics and directly integrated into Phenopackets as its primary phenotype vocabulary.
Key Features
- Terms are organised in a directed acyclic graph hierarchy covering all organ systems, with rich coverage of neurology and psychiatry including seizure types, cognitive phenotypes, movement disorders, and dementia.
- Terms are linked to OMIM, Orphanet, ClinVar, and DECIPHER disease databases.
- HPO is available in OWL and OBO formats for computational use.
- Releases are monthly with stable versioned term identifiers in the format HP:XXXXXXX.
Connections
- producedBy: Monarch Initiative
- correspondsWith: MP (HPO and the Mammalian Phenotype Ontology co-maintain a published cross-species phenotype mapping; neither is derived from the other)
- relatedTo: SNOMED CT (HPO and SNOMED CT cross-mapped for clinical phenotype coding)
- relatedTo: OMOP CDM (HPO terms used in OMOP CDM for phenotype-genotype associations)
- endorsedBy: OBO Foundry