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.
- Available in OWL and OBO formats for computational use.
- Releases are monthly with stable versioned term identifiers in the format HP:XXXXXXX.
Connections
- Integrated into: Phenopackets (primary phenotype vocabulary)
- Maps to: SNOMED CT, OMOP CDM (concept mapping)
- Part of: OBO Foundry