Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) - PubMed (original) (raw)

. 2002 Jan 1;30(1):69-72.

doi: 10.1093/nar/30.1.69.

Midori A Harris, Kara Dolinski, Catherine A Ball, Gail Binkley, Karen R Christie, Dianna G Fisk, Laurie Issel-Tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Weng, David Botstein, J Michael Cherry

Affiliations

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

Selina S Dwight et al. Nucleic Acids Res. 2002.

Abstract

The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over the last decade. As emphasis shifts from identification of the genes to identification of the role of their gene products in the cell, SGD seeks to provide its users with annotations that will allow relationships to be made between gene products, both within Saccharomyces cerevisiae and across species. To this end, SGD is annotating genes to the Gene Ontology (GO), a structured representation of biological knowledge that can be shared across species. The GO consists of three separate ontologies describing molecular function, biological process and cellular component. The goal is to use published information to associate each characterized S.cerevisiae gene product with one or more GO terms from each of the three ontologies. To be useful, this must be done in a manner that allows accurate associations based on experimental evidence, modifications to GO when necessary, and careful documentation of the annotations through evidence codes for given citations. Reaching this goal is an ongoing process at SGD. For information on the current progress of GO annotations at SGD and other participating databases, as well as a description of each of the three ontologies, please visit the GO Consortium page at http://www.geneontology.org. SGD gene associations to GO can be found by visiting our site at http://genome-www.stanford.edu/Saccharomyces/.

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Figures

Figure 1

Figure 1

GO display on the locus page at SGD. All existing GO terms to which a gene product has been annotated are listed on the gene product’s locus page. Clicking on an individual GO term gives a list of all other S.cerevisiae loci which are associated with the GO term, along with the published references and corresponding evidence codes used to make the associations. Clicking on ‘ASH1 GO evidence and references’ results in a more detailed page that provides the references and evidence codes for each ASH1 annotation (Fig. 2).

Figure 2

Figure 2

Evidence code and reference display for locus specific GO annotations. Clicking on ‘ASH1 GO evidence and references’ from the ASH1 locus page (Fig. 1) returns to a page which lists each GO term and the reference(s) and evidence code(s) used for each ASH1 specific GO association. Links to the SGD, PubMed and existing full text journal entries for each publication, as well as any associated Comments & Errata, are provided for each supporting reference. Note that annotation to a single GO term may be supported by more than one reference. In addition, a single reference may offer more than one type of evidence for the annotation, in which case each evidence code is provided along with a link to its definition and selected examples.

References

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