KnowEng, a Scalable Knowledge Engine for Large-Scale Genomic Data-OVERALL

描述(由申请人提供)：拟议的卓越中心的主要目标是为基因组学建立一个强大的、可扩展的知识引擎，KnowEnG。KnowEnG将通过整合源自最先进的数据挖掘和机器学习研究的多种分析方法，将现有关于基因之间关系的全面知识作为背景，并提供直观和专业设计的用户界面，从而改变生物医学研究人员分析全基因组数据的方式。为了实现这些目标，该项目包括以下部分：(1)收集现有的记录基因及其功能之间的联系的知识库，并将其整合成一个单一的知识网络；(2)开发计算方法，在现有知识的背景下分析全基因组用户数据集；(3)将这些方法落实到可扩展的软件组件中，这些组件可以部署在公共或私有云中；(4)基于HUBZero工具包，设计和实现一个基于Web的用户界面，能够以图形驱动和直观的方式对用户提供的数据集进行交互分析；(5)在临床科学(乳腺癌药物基因组学)、行为科学(确定行为模式背后的基因调控模块)和药物发现(基于基因组的微生物合成新生物活性化合物能力的预测)的三个大型项目中，彻底测试KnowEnG环境的功能性和有用性。KnowEng环境将部署在云基础设施中，并完全可供社区使用，中心开发的软件也将如此。拟建的中心是由计算科学和工程领域公认的世界领先者伊利诺伊大学(UIUC)和世界领先的临床护理和研究组织之一的梅奥诊所(Mayo Clinic)合作建立的，总部将设在伊利诺伊大学基因组生物学研究所，该研究所拥有最先进的设施和全国公认的基于多学科团队的基因组研究计划。

DESCRIPTION (provided by applicant): The primary goal of the proposed Center of Excellence is to build a powerful and scalable Knowledge Engine for Genomics, KnowEnG. KnowEnG will transform the way biomedical researchers analyze their genome-wide data by integrating multiple analytical methods derived from the most advanced data mining and machine learning research to use the full breadth of existing knowledge about the relationships between genes as background, and providing an intuitive and professionally designed user interface. In order to achieve these goals, the project includes the following components: (1) gathering and integrating existing knowledgebases documenting connections between genes and their functions into a single Knowledge Network; (2) developing computational methods for analyzing genome-wide user datasets in the context of this pre-existing knowledge; (3) implementing these methods into scalable software components that can be deployed in a public or private cloud; (4) designing and implementing a Web-based user interface, based on the HUBZero toolkit, that enables the interactive analysis of user-supplied datasets in a graphics-driven and intuitive fashion; (5) thoroughly testing the functionality and usefulness of the KnowEnG environment in three large scale projects in the clinical sciences (pharmacogenomics of breast cancer), behavioral sciences (identification of gene regulatory modules underlying behavioral patterns) and drug discovery (genome-based prediction of the capacity of microorganisms to synthesize novel biologically active compounds). The KnowEng environment will be deployed in a cloud infrastructure and fully available to the community, as will be the software developed by the Center. The proposed Center is a collaboration between the University of Illinois (UIUC), a recognized world leader in computational science and engineering, and the Mayo Clinic, one of the leading clinical care and research organizations in the worid, and will be based at the UIUC Institute for Genomic Biology, which has state-of-the-art facilities and a nationally recognized program of multidisciplinary team-based genomic research.