The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. This is accomplished primarily through OWL Axiomatization and OWL Reasoning.

The Monarch Initiative uses uPheno to group data from multiple species – for example:

Contributing Ontologies

  • mp* - mouse // mammal.owl
  • hp* - human // mammal.owl
  • zp - zebrafish** // vertebrate.owl
  • wbphenotype - C elegans // metazoa.owl
  • dpo* - Drosophila // metazoa.owl
  • fypo* - Fission Yeast // eukaryote.owl

* – this ontology provides their own OWL axiomatization
** – separately generated ontology


Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. BioMed Central; 2010 Jan 8;11(1):R2. PMCID: PMC2847714

Matentzoglu N, Osumi-Sutherland D, Balhoff JP, Bello S, Bradford Y, Cardmody L, Grove C, Harris MA, Harris N, Köhler S, McMurry J, Mungall C, Munoz-Torres M, Pilgrim C, Robb S, Robinson PN, Segerdell E, Vasilevsky N, Haendel M. uPheno 2: Framework for standardised representation of phenotypes across species. 2019 Apr 8.

See also