Ontology-based validation and identification of regulatory phenotypes

Research output: Contribution to journalArticle

Authors

Colleges, School and Institutes

External organisations

  • King Abdullah University of Science and Technology
  • University of Cambridge
  • University Hospitals Birmingham NHS Trust
  • NIHR Experimental Cancer Medicine Centre
  • NIHR Surgical Reconstruction and Microbiology Research Centre
  • NIHR Biomedical Research Centre

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 Fmax of up to 0.647. Availability and implementation https://github.com/bio-ontology-research-group/phenogocon.

Details

Original languageEnglish
Pages (from-to)i857-i865
JournalBioinformatics
Volume34
Issue number17
Publication statusPublished - 1 Sep 2018