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

摘要虽然生物数据库管理良好且相互关联丰富，但数据集成仍然是一个人工的、耗时的、容易出错的过程。该提案开发了一种计算基础设施，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。需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，这些查询又被转换为低级数据操作操作符；(2)可选拼接蛋白分析管道的规范和填充；(3)使用基于XML的包装器技术和中介器技术（IBM DB2 II）实现的中介测试平台。集成数据库之间存在的链接和路径度量可用于以对生物学家和数据管理员有用的方式描述查询结果，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不同的多条路径（结果基数）。成本模型和特定于领域和任务的语义用于选择生物管道的最佳路径或路径集。该研究解决了大规模数据共享的许多SEIII挑战。该项目解决了生物学家对数据库的探索；获取和利用领域特定知识；开发有效的方法来计算结果，设计和填充一个可公开访问的管道和网站。除了特定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访问和分析多个相互关联的异构资源的任务。

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.