Semantic Data Integration for Integrative Cancer Biology Research

描述(由申请人提供)：与癌症发生和发展相关的关键参数的高通量测量的最新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。为了实现由这种快速增长的信息带来的在综合癌症研究中取得巨大进步的前景，需要新的信息学工具来使研究人员有效地整合这些可用的数据。这项提议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，CBDI系统是一组caGrid服务和网格客户端应用程序，能够集成来自不同来源的数据和信息。CBDI系统旨在利用通过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强大的数据交换标准，通过提供caBIG语义的连贯本体视图来增强其使用，以便可以使用标准语义查询语言来查询数据源。CBDI系统包含一个本体视图生成器，用于使用Web Ontology Language(OWL)公开caBIG语义，以及一个分布式语义查询处理器，用于实现SemCDI查询模型，以使用SPARQL对caGrid数据服务执行基于RDF的查询。CBDI系统还能够整合由调查人员和研究机构收集的当地私人数据。提供多种可视化和概念搜索能力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查询从SPARQL到caBIG公共查询语言的转换。此外，通过系统组件的概念验证原型，论证了CBDI系统的总体可行性。在第二阶段，将在六个研究机构使用caBIG数据服务实施和测试完整的CBDI系统，评估其在各种真实世界运营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组与caBIG兼容的服务，这些服务制定了caBIG语义的一致本体论视图，以便可以在分布式caBIG兼容数据服务上使用SPARQL查询语言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.