The uPheno project aims to unify the annotation of phenotypes across species in a manner analogous to unification of gene function annotation by the Gene Ontology.
uPheno 2.0 builds on earlier efforts with a strategy that directly leverages the work of the phenotype ontology development community and incorporates phenotypes from a much wider range of species.
We have organised a collaborative community effort, including representatives of all major model organism databases, to document and align formal design patterns for representing phenotypes and further develop reference ontologies, such as PATO, which are used in these patterns.
A common development infrastructure makes it easy to use these design patterns to generate both species-specific ontologies and a species-independent layer that subsumes them.
The resulting community-curated ontology for the representation and integration of phenotypes across species serves two general purposes:
- Providing a community-developed framework for ontology editors to bootstrap, maintain and extend their phenotype ontologies in a scalable and standardised manner.
- Facilitating the retrieval and comparative analysis of species-specific phenotypes through a deep layer of species-independent phenotypes.
Currently, the development of uPheno is organized by a group that meets biweekly. See the meetings page for more info, including how to participate.