VO：疫苗本体论。

VO: The Vaccine Ontology.

作者信息

Zheng Jie, Lin Asiyah Yu, Huffman Anthony, Masci Anna Maria, Racz Rebecca, Wu Guanming, Roan Kallan, Ong Edison, Sarntivijai Sirarat, Hu Joy, Asfaw Eliyas, Kahn Hayleigh, Li Xingxian, Zhang Xumeng, Kosar Nilufer, Li Jianfu, Manuel Warren, Abeysinghe Rashmie, Rehana Hasin, Bansal Benu, Pan Yuanyi, Guo Jinjing, He Virginia, Song Justin, Seleznev Andrey I, Hur Katelyn, He Anna, Davydov Alexander, Yang Qi, Vita Randi, Peters Bjoern, Ruttenberg Alan, Diehl Alexander D, Hoyt Charles Tapley, Roncaglia Paola, Huntley Rachael P, Scheuermann Richard H, Courtot Melanie, Todd Thomas, Sayers Samantha, Chen Fang, Li Xinna, Yeh Feng-Yu, Xiang Zuoshuang, Ozgur Arzucan, Whetzel Patricia L, Musen Mark A, Mungall Christopher J, Leitner Wolfgang W, Cui Licong, Colby Lesley A, Mobley Harry L T, Athey Brian D, Omenn Gilbert S, Cowell Lindsay G, Tao Cui, Hur Junguk, Smith Barry, He Yongqun

机构信息

University of Michigan, Ann Arbor, MI, USA.

University of Texas MD Anderson Cancer Center, Houston, TX, USA.

出版信息

bioRxiv. 2025 Aug 15:2025.08.12.669998. doi: 10.1101/2025.08.12.669998.

DOI:10.1101/2025.08.12.669998

PMID:40832256

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12363946/

Abstract

With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly, we have since 2007 developed the community-based Vaccine Ontology (VO), which aligns with the Basic Formal Ontology and adheres to OBO Foundry principles. VO models ontologically vaccines, vaccine components, vaccine immune responses, vaccine investigation studies and other vaccine-related topics. VO represents more than 10,000 vaccines targeting 289 infectious pathogens and cancers in humans and over 30 nonhuman animal species. VO provides mappings to external resources such as RxNorm, CVX, FDA, and USDA. Various VO use cases exist. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). Semantic queries can be made to query VO. VO has been shown to enhance experimental and clinical vaccine data analysis and vaccine literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.

摘要

随着疫苗在研究和临床环境中的广泛应用，迫切需要对疫苗表示进行标准化，整合不同类型疫苗的信息，并支持计算机辅助推理。因此，自2007年以来，我们开发了基于社区的疫苗本体（VO），它与基础形式本体对齐并遵循OBO铸造厂原则。VO从本体上对疫苗、疫苗成分、疫苗免疫反应、疫苗研究以及其他与疫苗相关的主题进行建模。VO代表了针对人类289种传染病原体和癌症以及30多种非人类动物物种的10000多种疫苗。VO提供了与外部资源（如RxNorm、CVX、FDA和USDA）的映射。存在各种VO用例。VO促进了诸如小提琴疫苗数据库、ImmPort和疫苗佐剂汇编（VAC）等资源中的疫苗标准化。可以进行语义查询以查询VO。VO已被证明可增强实验和临床疫苗数据分析以及疫苗文献挖掘。总体而言，VO对疫苗建模和表示进行了标准化，并极大地支持了语义网时代的疫苗人工智能研究。