Limits...
Gene Ontology annotations at SGD: new data sources and annotation methods.

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM - Nucleic Acids Res. (2007)

Bottom Line: Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature.Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods.In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA, USA.

ABSTRACT
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

Show MeSH

Related in: MedlinePlus

Modifications to SGD interfaces to display the different GO annotation methods and data sources. (A) Manually curated and high-throughput GO annotations are individually listed on the Locus Summary, and the computational GO annotations are available by the ‘View Computational GO annotations’ hyperlink. (B) The phrase ‘GO Evidence and References’ hyperlinks to the GO Annotations page, which is subdivided into three sections listing the reference and evidence code for each annotation, as well as additional supporting data used to make the prediction, such as the InterPro domain and the source of the data. (C) From the Locus Summary and the GO Annotation pages, each GO term is hyperlinked to its GO Term page, which lists every gene annotated to that term in SGD and provides the definition, any synonyms and a graphical representation of the GO structure for that GO term. A table summarizes the number of genes annotated to that term using each annotation method, and includes links to download data. Below this table, the genes annotated to this term are listed along with their relevant reference, evidence code and annotation method.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238894&req=5

Figure 1: Modifications to SGD interfaces to display the different GO annotation methods and data sources. (A) Manually curated and high-throughput GO annotations are individually listed on the Locus Summary, and the computational GO annotations are available by the ‘View Computational GO annotations’ hyperlink. (B) The phrase ‘GO Evidence and References’ hyperlinks to the GO Annotations page, which is subdivided into three sections listing the reference and evidence code for each annotation, as well as additional supporting data used to make the prediction, such as the InterPro domain and the source of the data. (C) From the Locus Summary and the GO Annotation pages, each GO term is hyperlinked to its GO Term page, which lists every gene annotated to that term in SGD and provides the definition, any synonyms and a graphical representation of the GO structure for that GO term. A table summarizes the number of genes annotated to that term using each annotation method, and includes links to download data. Below this table, the genes annotated to this term are listed along with their relevant reference, evidence code and annotation method.

Mentions: The manually curated method indicates that the evidence in a publication has been individually reviewed to generate an annotation. Types of evidence can include experimental results in published literature that focuses on single genes or small sets of genes, author statements in a publication and sequence similarities that have been analyzed by the authors [for examples, see (12,13) shown in Figure 1B)].Figure 1.


Gene Ontology annotations at SGD: new data sources and annotation methods.

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM - Nucleic Acids Res. (2007)

Modifications to SGD interfaces to display the different GO annotation methods and data sources. (A) Manually curated and high-throughput GO annotations are individually listed on the Locus Summary, and the computational GO annotations are available by the ‘View Computational GO annotations’ hyperlink. (B) The phrase ‘GO Evidence and References’ hyperlinks to the GO Annotations page, which is subdivided into three sections listing the reference and evidence code for each annotation, as well as additional supporting data used to make the prediction, such as the InterPro domain and the source of the data. (C) From the Locus Summary and the GO Annotation pages, each GO term is hyperlinked to its GO Term page, which lists every gene annotated to that term in SGD and provides the definition, any synonyms and a graphical representation of the GO structure for that GO term. A table summarizes the number of genes annotated to that term using each annotation method, and includes links to download data. Below this table, the genes annotated to this term are listed along with their relevant reference, evidence code and annotation method.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238894&req=5

Figure 1: Modifications to SGD interfaces to display the different GO annotation methods and data sources. (A) Manually curated and high-throughput GO annotations are individually listed on the Locus Summary, and the computational GO annotations are available by the ‘View Computational GO annotations’ hyperlink. (B) The phrase ‘GO Evidence and References’ hyperlinks to the GO Annotations page, which is subdivided into three sections listing the reference and evidence code for each annotation, as well as additional supporting data used to make the prediction, such as the InterPro domain and the source of the data. (C) From the Locus Summary and the GO Annotation pages, each GO term is hyperlinked to its GO Term page, which lists every gene annotated to that term in SGD and provides the definition, any synonyms and a graphical representation of the GO structure for that GO term. A table summarizes the number of genes annotated to that term using each annotation method, and includes links to download data. Below this table, the genes annotated to this term are listed along with their relevant reference, evidence code and annotation method.
Mentions: The manually curated method indicates that the evidence in a publication has been individually reviewed to generate an annotation. Types of evidence can include experimental results in published literature that focuses on single genes or small sets of genes, author statements in a publication and sequence similarities that have been analyzed by the authors [for examples, see (12,13) shown in Figure 1B)].Figure 1.

Bottom Line: Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature.Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods.In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA, USA.

ABSTRACT
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

Show MeSH
Related in: MedlinePlus