Fundamentals of gene ontology functional annotation.
In: Alterovitz, G and Ramoni, M, (eds.)
Knowledge-Based Bioinformatics: From analysis to interpretation.
(173 - 208).
In this chapter we review the current approach to functional annotation, with particular emphasis on Gene Ontology (GO) annotation. Beginning with how the GO project was developed, we outline its particular format and features, and how it is used to annotate proteins from a wide range of species. The ontology development work that occurs alongside annotation and how a process-centric annotation approach results in larger scale ontology refinement will also be discussed. We will review the electronic mapping of GO terms from secondary data sources, for example protein motif databases, and how these annotations are displayed in the major GO browsers. We will also discuss a number of comparative genomics techniques that are being used to propagate GO annotations to orthologous and paralogous proteins in less well studied species. We include a brief overview of some of the other non-profit functional annotation efforts such as the IMEx Consortium and the Kyoto Encyclopedia of Genes and Genomes, and discuss how GO annotations are being integrated into these resources. In addition the inherent limitations associated with any protein annotation effort are discussed. Community participation is being actively sought as curators are faced with an ever increasing number of publications, and we outline some of the ways in which researchers can contribute to GO. We critically review and compare the mainstream GO browsers currently available (AmiGO, QuickGO), as well as discuss how to access GO annotations from some of the more specialised GO browsers such as The Cancer Genome Anatomy Project’s GO browser. A selection of the bioinformatic tools freely available to academic researchers is reviewed. These include third party tools allowing analysis of large scale experiments, and GO Consortium-developed tools which allow the download of GO annotations for sets of genes. We conclude with a review of the effect that functional gene annotation has had on biological data analysis. This book discusses knowledge-based and statistical approaches, along with applications in bioinformatics and systems biology.
|Title:||Fundamentals of gene ontology functional annotation|
|Keywords:||Bioinformatics, Gene Ontology|
|UCL classification:||UCL > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Cardiovascular Science|
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