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Abstract：
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
摘要：
COVID-19大流行促使了SARS-CoV-2病毒调查的巨大工作。快速，准确,因此，对生成数据的一致解释是最重要的问题。本体论-结构化，控制,词汇-旨在支持解释的一致性，从而防止数据孤岛的发展。本文描述了本体论如何在COVID-19研究领域为这一目的服务，通过遵循开放式生物和生物医学本体（OBO）铸造厂的原理，并重新使用现有的本体，例如传染病本体（IDO）核心，它提供了所有传染病调查所共有的术语内容。我们在这里报告IDO扩展的开发，病毒传染病本体论(VIDO)，涵盖病毒性传染病的参考本体论。我们激励术语和定义选择，展示现有OBO本体中术语的重用，说明本体论决策是如何被相关生命科学研究所激励的，并将VIDO连接到冠状病毒传染病本体论（CIDO）。接下来，我们使用这些本体论中的术语来注释SARS-CoV-2生命科学研究中的选择，强调了采用通用上层词汇的本体论如何无缝交织。最后,我们概述了未来的工作，包括目前正在开发的细菌和真菌传染病参考本体，然后引用VIDO和CIDO在宿主病原体数据分析中的用途，电子健康记录注释，和本体冲突解决项目。
