Collaborative Proposal: II+SEI Mediation Technology for Biological Pipeline Analysis

合作提案：用于生物管道分析的 II SEI 中介技术

• 批准号: 0430915
• 负责人: Louiqa Raschid
• 金额: $ 76.27万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-02-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0430915&HistoricalAwards=false
• 关键词: Collaborative; Proposal; II+SEI; Mediation; Technology

ABSTRACTWhile biological databases are well-curated and richly interconnected, data integration remains a manual, time-intensive, and error-prone process. The proposal develops a computational infrastructure that exploits biologists' domain expertise to express and execute data integration protocols for biological pipelines. Several challenges to be addressed include: (1) an exploration interface that can express high-level complex queries that in turn are translated into lower-level data manipulation operators, (2) the specification and population of an alternative splice protein analysis pipeline, and (3) a mediation testbed that is implemented using XML based wrapper technology and mediator technology (IBM DB2 II).The metrics of links and paths existing between integrated databases may be used to characterize query results in ways that are useful to biologists and data administrators and this proposal develops models to predict these metrics. Navigational queries require traversing multiple paths that differ in cost and benefit (result cardinality). Cost models and domain and task specific semantics are used to choose the best path or set of paths for a biological pipeline. The research addresses many of the SEIII challenges of large scale data sharing. The project addresses the exploration of databases by biologists; captures and exploits domain specific knowledge; develops efficient methodology to compute results and designs and populates a publicly accessible pipeline and website. The broader impact beyond the specific biological resources and protein pipeline is the development of a methodology and evaluation platform that can be applied to any task that requires access to, and analysis of, multiple inter-connected heterogeneous resources.

虽然生物数据库是精心策划和高度互联的，但数据集成仍然是一个手动的、耗时的、容易出错的过程。该提案开发了一个计算基础设施，利用生物学家的领域专业知识来表达和执行生物管道的数据集成协议。要解决的几个挑战包括：(1)可以表达高级复杂查询的探索接口，这些查询反过来被转换为低级数据操作操作符；(2)替代剪接蛋白质分析流水线的规范和填充；以及(3)使用基于XML的包装技术和中介技术(IBM DB2II)实现的中介试验床。集成数据库之间存在的链接和路径的度量可以用来以对生物学家和数据管理员有用的方式来表征查询结果，本提案开发了预测这些度量的模型。导航查询需要遍历成本和收益(结果基数)不同的多条路径。使用成本模型以及特定于域和任务的语义来选择生物管道的最佳路径或路径集。这项研究解决了大规模数据共享带来的许多SEIII挑战。该项目涉及生物学家对数据库的探索；获取和利用特定领域的知识；开发有效的方法来计算结果，并设计和建立一个可供公众访问的管道和网站。除了具体的生物资源和蛋白质管道之外，更广泛的影响是开发了一种方法和评估平台，可以应用于任何需要获取和分析多种相互关联的异质资源的任务。