Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

R E Foulger,P Le Mercier,B K Mcintosh,D Osumi-Sutherland,P Masson,C Hulo,S Poux,J Lomax

doi:10.1186/s12866-015-0481-x

R E Foulger, P Le Mercier + Show 6 more

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https://doi.org/10.1186/s12866-015-0481-x

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Abstract

BackgroundThe Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms.MethodsTo address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms.ConclusionsBuilding on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

Highlights

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner
The Gene Ontology (GO) project is a collaborative effort developing three ontologies to describe the molecular actions of a gene product, the biological process those actions are part of, and the cellular locations in which they are active
Subsequent to or in parallel with ontology construction, GO classes are associated with a gene product; this association is termed an annotation

Summary

Introduction

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. GO has since grown to be the most popular bio-ontology used for describing gene product characteristics [2, 3] It contains more than 40,000 terms, expressed using the W3C standard ontology language OWL2 [4]. GO annotation in particular has been used in analyses ranging from small-scale queries about a protein or pathway of interest to large-scale high-throughput studies including, among others, gene enrichment analyses, microarray analyses, predicting gene functions and textmining These analyses have allowed biologists to rapidly gain knowledge about their gene product or gene product set

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