Ontology-based Cross-species Integration and Analysis of Saccharomyces Cerevisiae Phenotypes

Overview

Journal J Biomed Semantics

Publisher Biomed Central

Specialties Biology
Biomedical Engineering

Date 2012 Oct 11

PMID 23046642

Citations 5

Authors

Georgios V Gkoutos

Robert Hoehndorf

Affiliations

Soon will be listed here.

Abstract

Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast.

Citing Articles

Semantic prioritization of novel causative genomic variants.

Boudellioua I, Mahamad Razali R, Kulmanov M, Hashish Y, Bajic V, Goncalves-Serra E PLoS Comput Biol. 2017; 13(4):e1005500.

PMID: 28414800 PMC: 5411092. DOI: 10.1371/journal.pcbi.1005500.

The anatomy of phenotype ontologies: principles, properties and applications.

Gkoutos G, Schofield P, Hoehndorf R Brief Bioinform. 2017; 19(5):1008-1021.

PMID: 28387809 PMC: 6169674. DOI: 10.1093/bib/bbx035.

The Drosophila anatomy ontology.

Costa M, Reeve S, Grumbling G, Osumi-Sutherland D J Biomed Semantics. 2013; 4(1):32.

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The Drosophila phenotype ontology.

Osumi-Sutherland D, Marygold S, Millburn G, McQuilton P, Ponting L, Stefancsik R J Biomed Semantics. 2013; 4(1):30.

PMID: 24138933 PMC: 3816596. DOI: 10.1186/2041-1480-4-30.

Systematic analysis of experimental phenotype data reveals gene functions.

Hoehndorf R, Hardy N, Osumi-Sutherland D, Tweedie S, Schofield P, Gkoutos G PLoS One. 2013; 8(4):e60847.

PMID: 23626672 PMC: 3628905. DOI: 10.1371/journal.pone.0060847.

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