Ontology-based validation and identification of regulatory phenotypes

Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Motivation Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations. Results We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can be resolved to improve overall annotation quality. We also apply our method to the rule-based prediction of regulatory phenotypes from functions and demonstrate that we can predict these phenotypes with F of up to 0.647. Availability and implementation https://github.com/bio-ontology-research-group/phenogocon.
Original languageEnglish (US)
Pages (from-to)i857-i865
Number of pages1
JournalBioinformatics
Volume34
Issue number17
DOIs
StatePublished - Sep 8 2018

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