uPheno — Unified Phenotype Ontology
Overview
The Unified Phenotype Ontology (uPheno) is a framework that integrates species-specific phenotype ontologies into a single, logically consistent cross-species representation. Developed within the Monarch Initiative, it provides a hierarchy of species-neutral phenotype terms under which counterparts from the human HPO, the Mammalian Phenotype Ontology (MP), and ontologies for zebrafish, fly, worm, and yeast are grouped. It supports cross-species inference such as identifying genes whose variants cause similar phenotypes in different organisms, which underpins variant prioritisation and model discovery for rare disease. The framework comprises the uPheno ontology, a community library of ontology design patterns for computable phenotype definitions, and standardised mapping tables between species-specific ontologies.
Composition
uPheno builds its phenotype definitions by reusing entity classes from established OBO Foundry ontologies, including UBERON for anatomy, the Cell Ontology for cell types, GO for biological processes and cellular components, ChEBI for chemical entities, and NBO for behaviour. The species-neutral terms are connected to their species-specific counterparts through logical axioms and SSSOM mapping tables, allowing phenotype data annotated in one organism’s ontology to be matched against another’s.
Connections
- producedBy: Monarch Initiative
- endorsedBy: OBO Foundry
- relatedTo: HPO (uPheno groups HPO human phenotype terms under species-neutral parents)
- relatedTo: MP (uPheno groups MP mouse phenotype terms under species-neutral parents)
Resources
- https://obophenotype.github.io/upheno
- https://github.com/obophenotype/upheno
- https://obofoundry.org/ontology/upheno.html
- https://doi.org/10.1101/2024.09.18.613276 (uPheno: a framework for cross-species integrative phenomics)