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Database (2009) Vol. 2009:bap010; doi:10.1093/database/bap010 published on September 29, 2009
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© The Author(s) 2009. Published by Oxford University Press.
This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

QuickGO: a user tutorial for the web-based Gene Ontology browser

Rachael P. Huntley*, David Binns, Emily Dimmer, Daniel Barrell, Claire O’Donovan and Rolf Apweiler

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

*Corresponding author: Tel: 01223 492515; Fax: +44 (0)1223 494468; Email: huntley{at}ebi.ac.uk


  Abstract

The Gene Ontology (GO) has proven to be a valuable resource for functional annotation of gene products. At well over 27 000 terms, the descriptiveness of GO has increased rapidly in line with the biological data it represents. Therefore, it is vital to be able to easily and quickly mine the functional information that has been made available through these GO terms being associated with gene products. QuickGO is a fast, web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. After undergoing a redevelopment, QuickGO is now able to offer many more features beyond simple browsing. Users have responded well to the new tool and given very positive feedback about its usefulness. This tutorial will demonstrate how some of these features could be useful to the researcher wanting to discover more about their dataset, particular areas of biology or to find new ways of directing their research.

Database URL: http://www.ebi.ac.uk/QuickGO

Abbreviations: Annotation, a specific association between a gene product and a Gene Ontology term. • Biological Process, one of the Gene Ontologies; terms describe a recognised series of events or molecular functions. • Cellular Component, one of the Gene Ontologies; terms describe where in the cell a gene product can be located. • Evidence Code, one of a number of three letter codes indicating how an annotation to a particular term is supported. • Gene Association File, a tab-delimited file containing all the information required for complete GO term-gene product associations. • GO browser, a computer tool designed for viewing the Gene Ontology and/or its associated gene product annotations. • GO slim, A subset of terms from the Gene Ontology used to provide a general overview of attributes for a set of gene products. • Molecular Function, one of the Gene Ontologies; terms describe the activities or jobs which a gene product can perform.

Received June 9, 2009; Revised July 10, 2009; Accepted July 12, 2009


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