Similarity-based search of model organism, disease and drug effect phenotypes.

Robert Hoehndorf,Paul N Schofield,Michael Gruenberger,Georgios V Gkoutos

doi:10.1186/s13326-015-0001-9

Abstract

BackgroundSemantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions, druggable therapeutic targets, and determination of pathogenicity.ResultsWe have developed PhenomeNET 2, a system that enables similarity-based searches over a large repository of phenotypes in real-time. It can be used to identify strains of model organisms that are phenotypically similar to human patients, diseases that are phenotypically similar to model organism phenotypes, or drug effect profiles that are similar to the phenotypes observed in a patient or model organism. PhenomeNET 2 is available at http://aber-owl.net/phenomenet.ConclusionsPhenotype-similarity searches can provide a powerful tool for the discovery and investigation of molecular mechanisms underlying an observed phenotypic manifestation. PhenomeNET 2 facilitates user-defined similarity searches and allows researchers to analyze their data within a large repository of human, mouse and rat phenotypes.

Highlights

Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions, druggable therapeutic targets, and determination of pathogenicity
We evaluated the performance of PhenomeNET 2 for prioritizing candidate genes of disease using rat phenotypes
A receiver operating characteristic (ROC) curve is a plot of the true positive rate as a function of the false positive rate, and is derived by comparing predicted associations against those asserted in the cognate model organism database

Summary

Results

We have developed PhenomeNET 2, a system that enables similarity-based searches over a large repository of phenotypes in real-time. It can be used to identify strains of model organisms that are phenotypically similar to human patients, diseases that are phenotypically similar to model organism phenotypes, or drug effect profiles that are similar to the phenotypes observed in a patient or model organism. PhenomeNET 2 is available at http://aber-owl. net/phenomenet

Conclusions

Background

Results and discussion