Realizing the potential of reference ontologies for the semantic web

描述(由申请人提供)：这项建议的动机是需要将大量复杂的生物医学信息整合到对生物功能的整体理解中，并将这种理解应用于改进的卫生保健。语义网被设想为在网络上层层分布的知识网络，它正在成为解决这一需求的重要组成部分，因为它将有助于确保不同的数据来源意味着相同的事情。软件的一个关键组件将是相互链接的本体网络，每个本体都是描述感兴趣领域的实体和关系的集合。目前，大多数本体都可以称为应用本体，因为它们是为特定的应用而设计的。然而，这些本体不能放大，它们经常相互重叠，而且由于不兼容的知识模型，它们很难链接在一起。参考本体，如我们的基本解剖模型(FMA)，是一种新兴的本体类型，有可能为将这些不同的应用本体链接到软件中提供概念基础。然而，由于它们的范围很大，引用本体非常复杂，应用程序开发人员很难使用。本提议的目的是通过开发用于从它们导出应用本体的方法来使这些参考本体易于使用，从而使它们可以发挥其作为语义网基础的潜力。我们将通过改编和扩展数据库社区的研究来做到这一点，以便1)创建应用本体作为参考本体上的视图，以及2)将这些视图嵌入为可查询的Web服务。在开发这些方法时，我们将与国家生物本体论中心(CBio)和密歇根大学计算机科学部合作，追求以下具体目标：1)研究和开发基于视图的方法，用于参考和应用本体之间的映射；2)设计和开发实现这些方法的软件工具；以及3)开发允许最终用户指定这些映射的图形界面。我们开发的工具将被整合为CBio生物门户框架的一个组成部分，用于访问相互关联的本体和数据。它们的开发和评估将主要由整合描述心脏功能的数据和计算模型的需求推动。

DESCRIPTION (provided by applicant): This proposal is motivated by the need to integrate vast amounts of complex biomedical information into a holistic understanding of biological function, and to apply that understanding to improved health care. The semantic web (SW), which is envisioned as a distributed network of knowledge layered on the web, is emerging as an essential part of the solution to this need since it will help to ensure that diverse sources of data mean the same thing. A critical component of the SW will be networks of interlinked ontologies, each of which is a collection of entities and relationships describing a domain of interest. At present most ontologies can be called application ontologies because they are designed for specific applications. However, these ontologies do not scale up, they often overlap with each other, and they are very difficult to link together because of incompatible knowledge models. Reference ontologies, such as our Foundational Model of Anatomy (FMA), are an emerging ontology type that have the potential to provide a conceptual foundation for linking together these diverse application ontologies into the SW. However, because their scope is so large reference ontologies are highly complex, and are very difficult for application developers to use. It is the purpose of this proposal to make such reference ontologies easy to use by developing methods for deriving application ontologies from them, so that they may fulfill their potential as a foundation for the semantic web. We will do this by adapting and extending research from the database community in order to 1) create application ontologies as views over reference ontologies, and 2) embed these views as query able web services. In developing these methods we will pursue the following specific aims, in collaboration with the National Center for Bio-ontology (CBio) and the UW computer science department: 1) investigate and develop view-based approaches for mapping between reference and application ontologies; 2) design and develop software tools that implement these approaches; and 3) develop graphical interfaces that allow end-users to specify these mappings. The tools we develop will be integrated as one component of the CBio Bio-Portal framework for accessing interlinked ontologies and data. Their development and evaluation will primarily be driven by the need to integrate data and computational models describing cardiac function.