Ontology-based validation and identification of regulatory phenotypes.

Kulmanov, Maxat and Schofield, Paul N and Gkoutos, Georgios V and Hoehndorf, Robert (2018) Ontology-based validation and identification of regulatory phenotypes. Bioinformatics (Oxford, England), 34 (17). i857-i865. ISSN 1367-4811. This article is available to all UHB staff and students via ASK Discovery tool http://tinyurl.com/z795c8c by using their UHB Athens login IDs

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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.

Item Type: Article
Additional Information: This article is available to all UHB staff and students via ASK Discovery tool http://tinyurl.com/z795c8c by using their UHB Athens login IDs
Subjects: QZ Pathology. Oncology
Divisions: Planned IP Care > Oncology and Clinical Haematology
Related URLs:
Depositing User: Mr Philip O'Reilly
Date Deposited: 07 Oct 2019 14:00
Last Modified: 07 Oct 2019 14:00
URI: http://www.repository.uhblibrary.co.uk/id/eprint/2457

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