QuickGO: a web-based tool for Gene Ontology searching

By David Binns, E. Dimmer, Rachael P. Huntley, Daniel Barrell, C. O’Donovan, Rolf Apweiler. Bioinform., 2009

916 citations recorded by the source corpus.

Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. Availability and Implementation: QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported. It can be queried online at http://www.ebi.ac.uk/QuickGO. The software for QuickGO is freely available under the Apache 2 licence and can be downloaded from http://www.ebi.ac.uk/QuickGO/installation.html Contact: goa@ebi.ac.uk; dbinns@ebi.ac.uk

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Citations in the corpus

A subcellular map of the human proteome (2017, methodology): “Gene Ontology terms and functional enrichment To check the overlap with GO annotations for proteins in the Cell Atlas, the web-based tool QuickGO (60) was used to acquire GO annotations for all genes using filters for cellular component and information source (downloaded 15 February 2017).”
The UniProt-GO Annotation database in 2011 (2011, background): “uk/QuickGO) (25), is the primary location for UniProt GO annotation data, where a full, weekly updated GO annotation set is D568 Nucleic Acids Research, 2012, Vol.”
RNAcentral: a hub of information for non-coding RNA sequences (2018, background): “These GO annotations are now displayed in the RNAcentral entries for the mature miRNAs (Figure 7), with links out to the QuickGO browser (23) for the full annotation records.”
Gene Ontology: Pitfalls, Biases, and Remedies. (2016, methodology): “The annotation extension data is available in the AmiGO (23) and QuickGO (24) browsers, as well as in the annotation files compliant with the GAF2.”
Exploring autophagy with Gene Ontology (2016, methodology): “Manual GO annotation was performed essentially as described by Patel et al.. 90 The most speci ﬁ c GO terms, representing the experimental data presented in each paper, were identi ﬁ ed using the AmiGO or QuickGO browsers 23,91,92 and a consistent annotation approach was used.”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, background): “In addition to sequences, RNAcentral provides a wide range of annotation types, such as genome coordinates, microRNA–target interactions (2,3), Gene Ontology (GO) terms (4), orthologs and paralogs (5), RNA family classification from Rfam (6) and more.”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, background): “SM Text 5 Evolution of ecologically relevant genes Analyses of ossification genes The gene list involved in the ossification was retrieved from quickGO (157).”