Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) organizes and displays molecular and genetic information about the genes and proteins of baker's yeast, Saccharomyces cerevisiae. Mutant phenotype screens have been the starting point for a large proportion of yeast molecular biological studies, and are still used today to elucidate the functions of uncharacterized genes and discover new roles for previously studied genes. To greatly facilitate searching and comparison of mutant phenotypes across genes, we have devised a new controlled-vocabulary system for capturing phenotype information. Each phenotype annotation is represented as an ‘observable’, which is the entity, or process that is observed, and a ‘qualifier’ that describes the change in that entity or process in the mutant (e.g. decreased, increased, or abnormal). Additional information about the mutant, such as strain background, allele name, conditions under which the phenotype is observed, or the identity of relevant chemicals, is captured in separate fields. For each gene, a summary of the mutant phenotype information is displayed on the Locus Summary page, and the complete information is displayed in tabular format on the Phenotype Details Page. All of the information is searchable and may also be downloaded in bulk using SGD's Batch Download Tool or Download Data Files Page. In the future, phenotypes will be integrated with other curated data to allow searching across different types of functional information, such as genetic and physical interaction data and Gene Ontology annotations.Database URL: http://www.yeastgenome.org/
Highlights
Mutant phenotypes, the outward manifestations of nucleotide sequence changes in the genome, are a key tool in elucidating the functions and roles of gene products.Saccharomyces cerevisiae has a rich store of mutant phenotype information, having been the subject of genetic experimentation for more than half a century in the laboratory and for thousands of years in popular use (1,2; http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/).In recent years, the development of a sophisticated genetic toolkit and the availability of a high-quality genome sequence have facilitated the generation of even more mutant phenotype data from large-scale genetic experiments
Saccharomyces Genome Database (SGD) provides comprehensive information about the yeast genome, including the complete genomic sequence as well as the biological roles of chromosomal features and gene products, all curated from the scientific literature [3]
To improve the breadth and accessibility of mutant phenotype information in SGD, over the past few years we have developed a system for recording and displaying mutant phenotypes that employs controlled vocabularies for the major concepts while retaining free-text fields to capture experimental details
Summary
The development of a sophisticated genetic toolkit and the availability of a high-quality genome sequence have facilitated the generation of even more mutant phenotype data from large-scale genetic experiments. SGD provides comprehensive information about the yeast genome, including the complete genomic sequence as well as the biological roles of chromosomal features and gene products, all curated from the scientific literature [3]. Various tools allow users to search the database in multiple ways in order to find, compare, and analyze sets of chromosomal features
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