Semantic Data Integration for Integrative Cancer Biology Research

描述（由申请人提供）：最近在与癌症发生和发展相关的关键参数的高通量测量方面取得了进展，导致公共和私人数据库中提供了丰富的癌症相关信息。为了实现这种快速扩展的信息所带来的综合癌症研究的巨大进步，需要新颖的信息学工具，使研究人员能够有效地整合这些可用的数据。该提案的主要目标是通过开发癌症生物学数据集成（CBDI）系统来增强对癌症过程的理解和建模，该系统是一个网格服务和网格客户端应用程序的集合，能够集成来自不同来源的数据和信息。CBDI系统旨在利用癌症生物医学信息网格（caBIG）倡议建立的丰富的语义元数据信息和健壮的数据交换标准，通过提供caBIG语义的连贯本体论视图来增强其使用，从而可以使用标准的语义查询语言查询数据源。CBDI系统包含一个本体视图生成器，用于使用Web本体语言（OWL）公开caBIG语义，以及一个分布式语义查询处理器，该处理器实现了semCDI查询模型，使用SPARQL对网格数据服务执行基于rdf的查询。CBDI系统还可以整合调查人员和研究机构收集的本地私人数据。提供多种可视化和概念搜索功能的直观用户界面用于构建查询和查看结果。在CBDI项目的第一阶段，开发了CBDI系统的关键算法和机制，包括本体视图的公开和将查询从SPARQL转换为caBIG的公共查询语言。此外，通过系统组件的概念验证原型验证了CBDI系统的总体可行性。在第二阶段，完整的CBDI系统将在六个研究机构使用caBIG数据服务进行实施和测试，评估其在各种实际操作条件和功能场景中的使用情况。公共卫生相关性：癌症生物学数据集成系统是一个与caBIG兼容的服务集合，它形成了caBIG语义的一致本体视图，因此可以使用SPARQL查询语言在分布式与caBIG兼容的数据服务上执行基于本体的查询。

DESCRIPTION (provided by applicant): Recent advances in high-throughput measurements of critical parameters related to cancer genesis and development have led to a wealth of cancer-related information available in public and private databases. To realize the promise of dramatic advancement in integrative cancer research enabled by this rapidly expanding information, novel informatics tools that allow researchers to efficiently integrate this available data are needed. The main objective of this proposal is to enable enhanced understanding and modeling of cancer processes through the development of the Cancer Biology Data Integration (CBDI) System, a collection of caGrid services and grid client applications capable of integrating data and information from disparate sources. The CBDI System aims to exploit the rich semantic metadata information and the robust data exchange standards established through the Cancer Biomedical Informatics Grid (caBIG) Initiative, enhancing its use through the provision of a coherent ontological view of caBIG semantics, so that data sources can be queried using a standard semantic query language. The CBDI System contains an Ontology View Generator to expose caBIG semantics using the Web Ontology Language (OWL) and a distributed Semantic Query Processor that implements the semCDI query model to execute RDF-based queries using SPARQL against caGrid data services. The CBDI System also enables the integration of local private data collected by investigators and research institutions. An intuitive user interface providing multiple visualization and concept searching abilities is used to build queries and view results. In Phase I of the CBDI project, key algorithms and mechanisms of the CBDI System were developed, including the exposure of ontology views and the conversion of queries from SPARQL into caBIG's common query language. In addition the overall feasibility of the CBDI System was demonstrated with proof-of-concept prototypes of system components. During Phase II, the complete CBDI System will be implemented and tested with caBIG data services at six research institutions, evaluating its use in a variety of real-world operating conditions and functional scenarios. PUBLIC HEALTH RELEVANCE: The Cancer Biology Data Integration System is a collection of caBIG-compatible services that formulate a coherent ontological view of caBIG semantics so that ontology-based queries can be performed using the SPARQL query language over distributed caBIG-compatible data services.