Realizing the potential of reference ontologies for the semantic web

描述（由申请人提供）：本提案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医疗保健。语义网（SW）被设想为在网络上分层的分布式知识网络，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来源的数据意味着相同的东西。软件的一个关键组成部分将是相互连接的本体网络，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程序设计的。然而，这些本体不能扩展，它们经常相互重叠，并且由于不兼容的知识模型，它们很难连接在一起。参考本体，例如我们的基础解剖学模型（FMA），是一种新兴的本体类型，它有可能为将这些不同的应用程序本体连接到软件中提供概念基础。然而，由于它们的范围非常大，引用本体非常复杂，并且对于应用程序开发人员来说非常难以使用。本提案的目的是通过开发从这些参考本体派生应用本体的方法，使这些参考本体易于使用，从而使它们能够发挥其作为语义web基础的潜力。我们将通过调整和扩展数据库社区的研究来实现这一点，以便：1)创建应用程序本体作为参考本体之上的视图，以及2)将这些视图嵌入为可查询的web服务。在开发这些方法的过程中，我们将与国家生物本体中心（CBio）和华盛顿大学计算机科学系合作，追求以下具体目标：1)研究和开发基于视图的方法，用于在参考本体和应用本体之间进行映射；2)设计和开发实现这些方法的软件工具；3)开发图形界面，允许最终用户指定这些映射。我们开发的工具将集成为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。它们的发展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驱动。

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.