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支持本体互操作性的可扩展本体开发(XOD)原则与工具实现。

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

作者信息

He Yongqun, Xiang Zuoshuang, Zheng Jie, Lin Yu, Overton James A, Ong Edison

机构信息

Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.

Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

出版信息

J Biomed Semantics. 2018 Jan 12;9(1):3. doi: 10.1186/s13326-017-0169-2.

Abstract

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

摘要

本体对于数据/元数据以及知识的标准化、共享和分析至关重要。随着数百种生物和生物医学本体的开发,确保本体的互操作性以及使用可互操作的本体进行标准化数据表示和集成变得至关重要。基于网络的Ontoanimal工具套件(例如,Ontofox、Ontorat和Ontobee)支持可扩展本体开发的不同方面。通过总结Ontoanimal和其他类似工具的共同特征,我们确定并提出了一种“可扩展本体开发”(XOD)策略及其相关的四项原则。这些XOD原则重用可靠本体中的现有术语和语义关系,开发并应用成熟的本体设计模式(ODP),并借助社区力量支持新本体的开发,促进标准化和可互操作的数据及知识表示与集成。采用XOD策略,再加上强大的XOD工具开发,将极大地支持本体的互操作性以及强大的本体应用,以支持数据具备可查找、可访问、可互操作和可重用(即FAIR)的特性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c12/5765662/45d9d5b407f2/13326_2017_169_Fig1_HTML.jpg

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