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M A Harris,
J Clark,
A Ireland,
J Lomax,
M Ashburner,
R Foulger,
K Eilbeck,
S Lewis,
B Marshall,
C Mungall, [......],
M Gwinn,
L Hannick,
J Wortman,
M Berriman,
V Wood,
N de la Cruz,
P Tonellato,
P Jaiswal,
T Seigfried,
R White
[show abstract]
[hide abstract]
ABSTRACT: The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
Nucleic Acids Research 02/2004; 32(Database issue):D258-61. · 8.03 Impact Factor
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M A Harris,
J Clark,
A Ireland,
J Lomax,
M Ashburner,
R Foulger,
K Eilbeck,
S Lewis,
B Marshall,
C Mungall, [......],
M Gwinn,
L Hannick,
J Wortman,
M Berriman,
V Wood,
N Cruz,
P Tonellato,
P Jaiswal,
T Seigfried,
R White
Nucleic Acids Res. 01/2004; 32(Database issue):258-261.
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Q. Dong,
Rama Balakrishnan,
G Binkley,
K.R. Christie,
M. Costanzo,
K Dolinski,
S S Dwight, S. Engel,
D.G. Fisk,
J. Hirschman,
E.L. Hong,
R. Nash,
L Issel-Tarver,
Anand Sethuraman,
C.L. Theesfeld,
S Weng,
D Botstein,
J M Cherry
[show abstract]
[hide abstract]
ABSTRACT: The budding yeast, Saccharomyces cerevisiae, has been experimentally manipulated for several decades. Much of the information generated is available in the Saccharomyces genome database (SGD, http://www.yeastgenome.org/). SGD contains large datasets of both genomic and proteomic information, as well as tools for data analysis. This paper will highlight three datasets that are maintained by SGD. First, a large dataset of hand-curated information is provided in machine readable format for each gene of the Saccharomyces genome. These hand-curated annotations use the gene ontology (GO) controlled vocabularies for biological process, molecular function and cellular component and each contains categorical evidence codes and literature references. A second area of focus is on metabolic pathways. A new dataset of hand-curated information on metabolic pathways within budding yeast was released in May 2003. This resource can be searched to view biochemical reactions and pathways and their component gene products. This resource also maps data from genome-wide expression analyses onto the pathway overview providing a visualization of the changes in gene expression in the context of cellular metabolism. These pathways are created and edited using the pathway tools software but the content is reviewed and updated by SGD. A third dataset has recently become available as the result of two comparative genomic analyses. Two groups sequenced the genomes of several yeasts closely related to S. cerevisiae, and then completed a gene-by-gene comparison of these genomes. These genome comparisons were combined with available experimental evidence by SGD. Using these data the annotations for the S.cerevisiae reference genome were improved. All these datasets are freely available from the SGD ftp site.
Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE; 09/2003
