QuickGO: a web-based tool for Gene Ontology browsing, interpretation and analysis
Creators: name: Shypitsyna, Aleksandra
name: Courtot, Melanie
name: Speretta, Elena
name: Holmes, Alexander
name: Sawford, Tony
name: Wardell, Tony
name: Sangya Pundir
name: Watkins, Xavier
name: Bingley, Mark
name: Antunes, Ricardo
name: Turner, Edward
name: Martin, Maria
name: O'Donovan, Claire
Publisher: name: F1000Research
Year: 2016

description: The Gene Ontology (GO) is a valuable resource for the functional annotation of gene products. In line with users' demands to accurately capture, interpret, analyze and evaluate the available functional information on genes and their attributes, its role in the scientific community is ever more important. GO is constantly expanding and improving to best represent our knowledge in various areas of biology, reflecting the development of new methods and the exponential growth of biosample resources and their experimental characterization. The current version of GO contains just under 45, 000 terms, to which over 250 million annotations have been made. It is therefore critical to be able to easily and quickly mine and visualise the available information. <br><br>The Gene Ontology Annotation (GOA) team would like to announce the release of a new version of our popular web-based tool for browsing and interpreting the GO and all associated annotations, QuickGO. <br><br>Benefiting from the constant communication with our international community (lab scientists, expert reviewers, bioinformaticians, clinicians and curators), the new QuickGO offers many more features in addition to improved speed, stability and data visualisation. Addressing the recent expansion of GO scope and aims, QuickGO now provides functional annotations not only to proteins, but also to protein complexes and RNA. The new user interface allows quick and easy searching of gene names, accessions, GO terms and annotations as well as evidence codes – recently connected to the Evidence Code Ontology. The interface, as proven by extensive user testing, is friendly and highly intuitive for users with different levels of GO experience. Additionally, it provides integrated contextual help covering all aspects of functionality. <br><br>Following the needs and requests of the scientific community contributing to and employing GO data, the filtering options in QuickGO have been significantly redesigned. The basic and most popular filters can now be applied directly while visualizing annotations of interest, while experienced users have access to advanced filters to retrieve, interpret and further analyze their datasets.<br><br>The front page of the QuickGO browser has direct links to major functions, including our GO slimming wizard. This tool allows mapping of the more GO granular terms to a smaller number of higher level, broader parent terms, and thus enables a quick overview of a genome or the large experimental datasets, of utmost importance for GO enrichment analysis. The wizard's design has been completely redeveloped to focus on simplicity and intuitive browsing, while preserving its accuracy and functionality. <br><br>The release of this new version of QuickGO, powered by recent innovations in technology, reflects the development of GO and biological sciences. It addresses the various needs of our users from contributing to GO annotation to applying it to discover functional information about genes and gene products, interpreting the results from the particular biological disciplines or looking for new ways to direct research.