新型冠状病毒肺炎领域本体构建及应用

Construction and application of a COVID-19 ontology

目的 构建一个开放、全面、语义表达良好的新型冠状病毒肺炎(COVID-19)领域本体,用于支持COVID-19相关知识的共享和有效利用。方法 在生物医学顶层本体基本形式化本体(BFO)框架下,使用斯坦福大学七步法,利用Protégé和Ontofox工具,通过抽取国内外现有本体、知识库和诊疗指南中的COVID-19相关知识并加以重新组织,构建COVID-19领域本体,并使用推理机和文献抽样调查法对本体进行质量评价。结果 在冠状病毒传染性疾病本体(CIDO)的基础上,扩展了症状、预防、临床诊疗和药物等方面内容,构建了一个覆盖疾病、诊断、病因、病毒、传播、症状、治疗、药物、预防等方面知识的COVID-19领域本体(CIDO-COVID-19)。推理机验证结果表明,该本体具有较好的一致性,文献抽样显示其具有较高的术语覆盖率,并利用该本体指导开发了一个COVID-19知识图谱原型。结论 CIDO-COVID-19实现了COVID-19领域知识的整合与复用,具有较好的一致性和术语覆盖率,可用于支持本领域的知识库构建和知识服务。

Objective To construct an open,comprehensive and well-expressed coronavirus disease 2019(COVID-19ontology to facilitate the sharing and effective use of COVID-19 knowledge. Methods Under the framework of the top-level biomedical ontology Basic Formal Ontology(BFO),a COVID-19 ontology was constructed using Stanford′s seven-step method,Protégé and Ontofox tools and by retrieving and reorganizing COVID-19 related knowledge from existing ontologies,knowledge bases,and diagnosis and treatment guidelines. The reasoner and literature sampling survey method was employed to assess the quality of the ontology. Results On the basis of the Coronavirus Infectious Disease Ontology(CIDO),the content related to symptoms,prevention,clinical diagnosis and treatment and drugs was expanded,and an ontology for COVID-19(CIDO-COVID-19),which covers the knowledge of diseases,diagnosis,etiology,viruses,transmission,symptoms,treatment,drugs and prevention was constructed. Reasoner verification results showed that CIDO-COVID-19 had good consistency,and literature sampling analysis showed that the ontology had a high term coverage.A prototype of the knowledge graph of COVID-19 was developed under the guidance of CIDO-COVID-19. Conclusion CIDO-COVID-19 is capable of the integration and reuse of knowledge of COVID-19,with good consistency and terminology coverage,which can be used to support the construction of knowledge bases and knowledge services.