Pathak Jyotishman, Johnson Thomas M, Chute Christopher G
Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
Integr Comput Aided Eng. 2009 Aug;16(3):225-242. doi: 10.3233/ICA-2009-0315.
In the past several years, various ontologies and terminologies such as the Gene Ontology have been developed to enable interoperability across multiple diverse medical information systems. They provide a standard way of representing terms and concepts thereby supporting easy transmission and interpretation of data for various applications. However, with their growing utilization, not only has the number of available ontologies increased considerably, but they are also becoming larger and more complex to manage. Toward this end, a growing body of work is emerging in the area of modular ontologies where the emphasis is on either extracting and managing "modules" of an ontology relevant to a particular application scenario (ontology decomposition) or developing them independently and integrating into a larger ontology (ontology composition). In this paper, we investigate state-of-the-art approaches in modular ontologies focusing on techniques that are based on rigorous logical formalisms as well as well-studied graph theories. We analyze and compare how such approaches can be leveraged in developing tools and applications in the biomedical domain. We conclude by highlighting some of the limitations of the modular ontology formalisms and put forward additional requirements to steer their future development.
在过去几年里，已经开发了各种本体和术语，如基因本体，以实现多个不同医学信息系统之间的互操作性。它们提供了一种表示术语和概念的标准方式，从而支持为各种应用轻松传输和解释数据。然而，随着它们的使用越来越广泛，不仅可用本体的数量大幅增加，而且它们也变得越来越大且更难管理。为此，模块化本体领域正在涌现越来越多的工作，其重点要么是提取和管理与特定应用场景相关的本体“模块”（本体分解），要么是独立开发它们并集成到更大的本体中（本体合成）。在本文中，我们研究模块化本体的最新方法，重点关注基于严格逻辑形式主义以及经过充分研究的图论的技术。我们分析并比较如何在生物医学领域开发工具和应用中利用这些方法。我们通过强调模块化本体形式主义的一些局限性来得出结论，并提出额外的要求以指导它们未来的发展。
