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开发一种计算机化系统，能够整合来自不同来源的数据和信息，以便能够增强癌症过程的模型。该系统旨在利用和扩展癌症生物医学信息网格(CaBIG)的功能，允许用户和应用程序以新颖的方式利用caBIG中包含的丰富语义信息，在概念层面上对癌症相关数据源进行查询。该系统包含使用Web Ontology Language(OWL)公开这些语义的机制，并使用SPARQL构建和执行基于RDF的查询，从而自动识别要在网格中查询的数据服务。提供多种可视化和概念搜索能力的直观用户界面用于建立查询和查看结果，同时还通过语义网标准为计算机与计算机的交互提供编程界面。在我们的提案的第一阶段，我们将开发所提出的系统的主要算法和机制，包括本体视图的公开和查询从SPARQL到caBIG的通用查询语言的转换，并将测试概念验证原型以证明我们设计的可行性。癌症生物学数据集成系统是一个信息集成解决方案，使用户能够以更接近于陈述研究问题的方式使用概念抽象来查询与癌症相关的数据。它将癌症生物医学信息网格(CaBIG)中包含的丰富语义信息建模为本体视图，并使用语义Web标准创建和执行对与caBIG兼容的数据源的查询。

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 the development of a computerized system capable of integrating data and information from disparate sources in order to enable enhanced models of cancer processes. The proposed system aims to use and expand the capabilities of the Cancer Biomedical Informatics Grid (caBIG) to allow users and applications to perform queries on cancer-related data sources at a conceptual level, utilizing the rich semantic information contained in caBIG in novel ways. The system contains mechanisms to expose these semantics using the Web Ontology Language (OWL), and to build and execute RDF-based querying using SPARQL, automatically identifying data services to query within the grid. An intuitive user interface providing multiple visualization and concept searching abilities is used to build queries and view results, while a programmatic interface is also provided for computer-to-computer interaction through Semantic Web standards. In Phase I of our proposal, the main algorithms and mechanisms of the proposed system, including the exposure of ontology views and the conversion of queries from SPARQL into caBIG's common query language will be developed, and proof-of-concept prototypes will be tested to prove the feasibility of our design.The Cancer Biology Data Integration System is an information integration solution that enables users to query cancer-related data using conceptual abstractions in a declarative manner more closely resembling the way in which research questions are stated. It models the rich semantic information contained in the Cancer Biomedical Informatics Grid (caBIG) as an ontology view, and uses Semantic Web standards to create and execute queries into caBIG-compatible data sources.