PathSys: integrating molecular interaction graphs for systems biology
PathSys: integrating molecular interaction graphs for systems biology
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DOI：
10.1186/1471-2105-7-55
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发表时间：
2006-02-07
影响因子：
3
通讯作者：
Gupta, A
中科院分区：
文献类型：
--
作者：
Baitaluk, M;Qian, XF;Gupta, A
背景资料：系统生物学中信息集成的目标是将来自多个数据库和数据集（从高通量和低通量实验中获得）的信息联合收割机组合在一个数据管理方案下，以便累积的信息提供比单独考虑单个信息源可能提供的更大的生物学见解。结果：在这里，我们提出了PathSys，一个基于图形的系统，用于创建一个组合的数据库的网络的互动，以产生综合的生物机制的看法。我们使用PathSys整合了超过14个策划和公开贡献的数据源，用于芽殖酵母（S。酿酒酵母）和基因本体。一些探索性的问题，制定了一个综合数据库的关系和图形为基础的查询相结合。因此，PathSys是一个通用的、可扩展的生物信息图形数据仓库，具有图形操作和查询语言、存储机制和通过模式映射的通用数据导入机制。几项测试研究的结果证明了该方法在检索基因和蛋白质之间的生物学有趣关系，连接它们的网络，以及PathSys作为用于交互网络集成的可扩展的基于图的仓库和假设生成器系统的效用。PathSys的客户端软件名为BiologicalNetworks，是为分子网络的导航和分析而开发的，可以在http://brak.sdsc.edu/pub/BiologicalNetworks上以Java Web Start应用程序的形式获得。
Background: The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.Results: Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast ( S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.Conclusion: Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.