数据整合论文：数据整合 XML 生物数据库 生物通路.docVIP

【关键词】数据整合 XML 生物数据库 生物通路 【英文关键词】Data integration XML Biological database Biological pathway 数据整合论文：生物信息学数据整合的应用研究 【中文摘要】本文以系统生物学建模工具COSBI-Model为出发点，扩展了其数据整合功能，整合了外部数据库通路模型，并采用中间件模式、GAV映射方法设计与整合数据库，将整合应用程序作为Web服务进行发布，这些工作实现了生物信息学数据整合的部分应用。然而，生物信息学发展日新月异，使得数据整合面临极大的挑战，数据库存储模式需要统一规范，系统生物学中系统模型语言需要统一格式，很多问题都说明公认的中间管道的开发需要生物信息学专家的深入研究。本文的意义在于满足了生物学家建立系统生物模型过程中的信息需求，扩展了建模工具COSBI-Model对外部数据库通路信息的整合功能实现。本文自主设计并实现了来自不同数据库的生物通路的数据整合与引入过程，通过引入外部数据库的相关生物通路模型，为系统生物学家进行下一步的计算机模拟提供了便捷的技术支持。通过对XML文件的分析处理，采用C#语言编写了用户友好的图形界面接口。首先对XML文件进行预处理，调整过滤其模式和内容，达到可以与建模工具匹配的形式；其次调研通路模型与建模工具之间的联系，定义相关的整合规则；然后在C#环境下通过模型提供的模型软件包及相关的XML解析技术，将模型信息整合到COSBI-Model中；当整合软件基本完成之后，将其作为Web服务发布到网络中供生物学家使用。 【英文摘要】Data integration is an open challenge in bioinformatics. Represented by the human genomicproject, the genomics era has generated and speed-up generating huge amount of biologicaldata. From DNA, RNA, SNP, protein to metabolic pathway network and so on, data fromnearly every level of organism are facing explosive growth. It is a very useful source for thebiologists, but opportunity and challenge exist together, facing the huge and growing amountof available biological data, the problem of biology data integration (that is, modelling,storing and querying) is now considered as a bottleneck in many biology researches. Astandard and accepted middle tunnel model is necessary for the realization of data integration.COSBI-Model is a simple and programming language-based modeling tool withuser-friendly interface. It has provides the biologists lots of convenient to model andcooperated with other software for simulation, and it has a wide prospect as a processcalculi-based modeling tool. But it has some shortage, like the function of integration. It couldnot provide reference model and outside information at runtime, so the extension of thedatabase-based integration ability to COSBI-Model is an urgent question to the designers.Moreover, depending on different interests of collectors and differ