Department of Bioinformatics, University Medical Center Göttingen Göttingen, Germany ; Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen Göttingen, Germany.
Front Genet. 2012 Oct 5;3:197. doi: 10.3389/fgene.2012.00197. eCollection 2012.
The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.
语义网依赖于本体论的使用，以便电子系统解释上下文信息。理想情况下，本体论的处理和访问应该对用户完全透明。为此，我们开发了一种服务，旨在弥合特定知识领域的专家、本体论者和应用程序开发人员之间的差距。这里介绍的基于本体的答案（OBA）服务可以嵌入到自定义应用程序中，以访问本体的类及其关系作为最重要的结构特征，以及关系中编码的信息本体类之间。因此，计算生物学家可以受益于本体，而无需详细了解各自的本体。本体的内容被映射到一个连接对象的图中，该图与 Java 中的面向对象编程风格兼容。语义功能实现了对本体复杂语义的知识，超越了类层次结构和“部分”关系。通过使用这些 OBA 功能，应用程序可以提供语义搜索功能，或者（在概述的示例中）将解剖结构映射到所属的器官。语义功能通过实现所需的知识，减轻了应用程序开发人员对使用的本体的语义和管理指南的深入了解的必要性。OBA 服务的架构封装了处理本体的逻辑，以实现与应用程序逻辑的分离。带有当前插件的公共服务器可用，并可在自定义应用程序中与提供的连接器一起使用，场景类似于呈现的用例。如果项目需要使用自定义插件或非公共本体，则服务器和客户端都是免费提供的。OBA 服务和进一步的文档可在 http://www.bioinf.med.uni-goettingen.de/projects/oba 获得。
