Gene Ontology annotation quality analysis in model eukaryotes

Nucleic Acids Research
Teresia J BuzaShane C Burgess

Abstract

Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers' ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases).

References

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Dec 1, 2006·Nucleic Acids Research·Fiona M McCarthyShane C Burgess

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Citations

Dec 17, 2009·Omics : a Journal of Integrative Biology·Gil StelzerDoron Lancet
Mar 4, 2009·Bioinformatics·Mark F Rogers, Asa Ben-Hur
Nov 16, 2010·Nucleic Acids Research·Fiona M McCarthyShane C Burgess
Dec 27, 2011·Plant Physiology·Michiel Van BelKlaas Vandepoele
Oct 27, 2009·BMC Bioinformatics·Arye HarelDoron Lancet
Oct 14, 2009·BMC Bioinformatics·Teresia J BuzaFiona M McCarthy
Oct 14, 2009·BMC Bioinformatics·Lauren A BrightFiona M McCarthy
Oct 14, 2009·BMC Bioinformatics·Bart H J van den BergSusan M Bridges
Jun 9, 2012·BMC Bioinformatics·Leila Ranandeh KalankeshAndy Brass
May 7, 2009·Genome Biology·Tamir TullerEytan Ruppin
Jun 14, 2012·PLoS Computational Biology·Nives SkuncaChristophe Dessimoz
Jan 1, 2009·PloS One·Emily J CapraLeonid Kruglyak
Feb 12, 2011·PloS One·Hiren KarathiaRui Alves
Mar 4, 2009·Bioinformation·Siva Prasad AkulaSrinubabu Gedela
Jun 7, 2014·Database : the Journal of Biological Databases and Curation·Maria TaboadaMaría Jesús Sobrido
May 15, 2015·PloS One·Nivedita RangarajanSridhar Hannenhalli
Jan 13, 2015·Journal of Industrial Microbiology & Biotechnology·Evangelos Simeonidis, Nathan D Price
Jan 11, 2013·BMC Genomics·Chia-Lang Hsu, Ueng-Cheng Yang
May 12, 2020·Frontiers in Genetics·Yingwen ZhaoGuoxian Yu
Jul 4, 2021·Clinical Pharmacology and Therapeutics·Michelle Whirl-CarrilloTeri E Klein
Aug 28, 2021·Insects·Surya SahaFiona M McCarthy

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Methods Mentioned

BETA
ISS

Software Mentioned

GOPubMed
house Perl scripts
GAQ
DAGdepth
GOSlim
GoSlimViewer
Generic
ISS

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