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. 2012 Jan;40(Database issue):D1262-9.
doi: 10.1093/nar/gkr907. Epub 2011 Nov 22.

GONUTS: the Gene Ontology Normal Usage Tracking System

Daniel P Renfro  1 , Brenley K McIntosh, Anand Venkatraman, Deborah A Siegele, James C Hu
Affiliations

GONUTS: the Gene Ontology Normal Usage Tracking System

Daniel P Renfro et al. Nucleic Acids Res. 2012 Jan.

Abstract

The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins. GONUTS uses wiki technology to allow registered users to share and edit notes on the use of each term in GO, and to contribute annotations for specific genes of interest. By providing a site for generation of third-party documentation at the granularity of individual terms, GONUTS complements the official documentation of the Gene Ontology Consortium. To provide examples for community users, GONUTS displays the complete GO annotations from seven model organisms: Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Arabidopsis thaliana. To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt. GONUTS will improve the consistency of annotation efforts across genome projects, and should be useful in training new annotators and consumers in the production of GO annotations and the use of GO terms. GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request.

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Figures

Figure 1.
Figure 1.
A typical GO term page in GONUTS. (A) Information about the GO term derived from the ontology files from the GO consortium, including id, definition, relationships, and parent terms. (B) A ontology graph from the EBI. (C) User-edited section for notes. In this example, a user has embedded an uploaded diagram explaining the term in better detail. (D) Child Terms (E) Genes annotated to this term. The page also contains all the typical elements of a MediaWiki page including a sidebar for site-navigation and tabs along the top for various actions.
Figure 2.
Figure 2.
A user-created GONUTS page for E. coli ihfB generated from its UniProt record.
Figure 3.
Figure 3.
Screenshots of a user-created annotation jamboree category page for human SMAD signaling proteins started as part of the cardiovascular GO annotation initiative. Genes of interest are placed in the jamboree category. An extension generates a sortable and filterable table (A) and diagrams showing the annotations made to genes in this category (B). The table is truncated in this figure and only one of the three diagrams is shown. The full page can be viewed at (http://gowiki.tamu.edu/wiki/index.php/Category:SMAD_signaling).
Figure 4.
Figure 4.
Distribution of user contributions to GONUTS. Contributed revisions are grouped in bins of 10. Users with no edits are not shown.
See this image and copyright information in PMC

References

    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. - PMC - PubMed
    1. Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res. 2001;11:1425–1433. - PMC - PubMed
    1. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32:D258–D261. - PMC - PubMed
    1. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009–an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 2009;37:D396–D403. - PMC - PubMed
    1. Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R. QuickGO: a user tutorial for the web-based Gene Ontology browser. Database (Oxford) 2009;2009:bap010. - PMC - PubMed

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