New mutant phenotype data curation system in the Saccharomyces Genome Database
New mutant phenotype data curation system in the Saccharomyces Genome Database
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DOI：
10.1093/database/bap001
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发表时间：
2009-01-01
影响因子：
5.8
通讯作者：
Cherry, J. Michael
中科院分区：
文献类型：
--
作者：
Costanzo, Maria C.;Skrzypek, Marek S.;Cherry, J. Michael
酵母基因组数据库（SGD; http：//www.yeastgenome.org/）组织并显示关于面包酵母（酿酒酵母）的基因和蛋白质的分子和遗传信息。突变体表型筛选一直是大部分酵母分子生物学研究的起点，并且今天仍然用于阐明未表征基因的功能和发现先前研究的基因的新作用。为了极大地促进跨基因突变表型的搜索和比较，我们设计了一个新的受控词汇系统来捕获表型信息。每个表型注释被表示为“可观察的”，其是被观察到的实体或过程，以及描述突变体中该实体或过程的变化的“限定符”（例如，“可观察的”）。G.减少、增加或异常）。有关突变体的其他信息，如菌株背景、等位基因名称、观察到表型的条件或相关化学物质的身份，均在单独的字段中捕获。对于每个基因，突变表型信息的汇总显示在基因座汇总页面上，完整信息以表格形式显示在表型详细信息页面上。所有的信息都是可搜索的，也可以使用SGD的批量下载工具或下载数据文件页面批量下载。未来，表型将与其他精选数据整合，以允许搜索不同类型的功能信息，例如遗传和物理相互作用数据以及Gene Ontology注释。数据库URL：http://www.yeastgenome.org/
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/