A Knowledge Base for Storage and Analysis of Expressed Sequence Tags (ESTs)

表达序列标签 (EST) 存储和分析的知识库

• 批准号: 0092336
• 负责人: Carl Schmidt
• 金额: $ 53.83万
• 依托单位: University of Delaware
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-02-15 至 2005-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0092336&HistoricalAwards=false
• 关键词: Knowledge; Base; Storage; Analysis; Expressed

Expressed sequence tags (EST's), are short nucleotide sequences determined from the cDNA copy of mRNA in a given cell, tissue, organ, or organism. EST's are widely used and equally widely generated, providing information about gene identity, expression and distribution for a wide range of organisms. Although it is relatively easy to generate the sequence information of an EST, there are a number of problems associated with storing and using the information. The software platform proposed here integrates a database, a biological ontology, or structured language, and sequence analysis functions for an EST knowledge base. This knowledge base addresses three problems faced by a biologist: storage of the data, analysis and archiving of the results, and integration into a cumulative database. The system is designed to permit a typical biologist to install and operate it. In order to do this, the system will provide user-friendly interfaces for additon of sequences, automated running of assembly and analysis programs, a query and alert system for complex searches, and a data sharing arrangement for geographically separate laboratories to permit integration. As a prototype, a knowledge base on the chicken will be developed. This is particularly useful since the chicken is often used as a comparative species for contrasting with mammals such as mouse and human. In developing the system, a range of training opportunities will be offered to undergraduates, graduates and postdoctoral scientists.

表达序列标签（EST）是从给定细胞、组织、器官或生物体中mRNA的cDNA拷贝确定的短核苷酸序列。 EST被广泛使用，产生也同样广泛，为广泛的生物体提供有关基因身份、表达和分布的信息。 虽然产生EST的序列信息相对容易，但存在与存储和使用信息相关的许多问题。 这里提出的软件平台集成了一个数据库，生物本体，或结构化语言，和EST知识库的序列分析功能。 该知识库解决了生物学家面临的三个问题：数据的存储，结果的分析和存档，以及集成到累积数据库中。 该系统的设计允许一个典型的生物学家安装和操作它，为了做到这一点，该系统将提供用户友好的界面，用于添加序列，自动运行的组装和分析程序，查询和警报系统，为复杂的搜索，和数据共享的安排，地理上不同的实验室，以允许集成。 作为一个原型，将开发一个关于鸡的知识库。 这是特别有用的，因为鸡经常被用作与哺乳动物如小鼠和人进行对比的比较物种。在开发该系统时，将向本科生、研究生和博士后科学家提供一系列培训机会。