VO: The Vaccine Ontology

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

doi:10.1038/s41597-026-07298-w

VO: The Vaccine Ontology

Jie Zheng
, Asiyah Yu Lin
, Anthony Huffman
, Anna Maria Masci
, Rebecca Racz
, Guanming Wu
, Kallan Roan
, Edison Ong
, Sirarat Sarntivijai
, Joy Hu
, Eliyas Asfaw
, Hayleigh Kahn
, Xingxian Li
, Xumeng Zhang
, Joshua Monickaraj
, Nilufer Kosar
, Jianfu Li
, Warren Manuel
, Rashmie Abeysinghe
, Hasin Rehana

Benu Bansal, Yuanyi Pan, Jinjing Guo, Virginia He, Justin Song, Andrey I. Seleznev, Katelyn Hur, Anna He, Alexander Davydov, Qi Yang, Anna Ostropolets, Randi Vita, Bjoern Peters, Alan Ruttenberg, Alexander D. Diehl, Charles Tapley Hoyt, Paola Roncaglia, Rachael P. Huntley, Richard H. Scheuermann, Melanie Courtot, Thomas Todd, Samantha Sayers, Fang Chen, Xinna Li, Feng Yu Yeh, Zuoshuang Xiang, Arzucan Ozgur, Patricia L. Whetzel, Mark A. Musen, Christopher J. Mungall, Wolfgang W. Leitner, Licong Cui, Lesley A. Colby, Harry L.T. Mobley, Brian D. Athey, Gilbert S. Omenn, Lindsay G. Cowell, Cui Tao, Junguk Hur, Barry Smith, Yongqun He

University of Michigan, Ann Arbor
University of Texas MD Anderson Cancer Center
Oregon Health and Science University
Boehringer Ingelheim GmbH
University of Maryland, College Park
Mayo Clinic Florida
University of Texas Health Science Center at Houston
University of North Dakota
Brown University
University of Pittsburgh
Red River High School
Huron High School
Thesaurus Health
IQVIA Inc.
Johnson & Johnson
Columbia University
La Jolla Institute for Allergy and Immunology
SUNY Buffalo
RWTH Aachen University
Elsevier Limited
National Institutes of Health
Ontario Institute for Cancer Research
University of Houston
University of North Carolina at Chapel Hill
Stanford University
Lawrence Berkeley National Laboratory
University of Texas Southwestern Medical Center

Research output: Contribution to journal › Article › peer-review

Abstract

Vaccines are widely used in both research and clinical settings. To facilitate FAIR data practices, we urgently 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 ontologically models 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. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). VO enables semantic queries on vaccine data. It has been shown to enhance the analysis of experimental and clinical vaccine datasets, as well as vaccine-related literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.

Original language	English
Article number	994
Journal	Scientific Data
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41597-026-07298-w
State	Published - Dec 2026

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@article{380cfe56750a477aaef2770cf7ceacb9,

title = "VO: The Vaccine Ontology",

abstract = "Vaccines are widely used in both research and clinical settings. To facilitate FAIR data practices, we urgently 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 ontologically models 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. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). VO enables semantic queries on vaccine data. It has been shown to enhance the analysis of experimental and clinical vaccine datasets, as well as vaccine-related literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.",

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

note = "Publisher Copyright: {\textcopyright} The Author(s) 2026.",

year = "2026",

month = dec,

doi = "10.1038/s41597-026-07298-w",

language = "English",

volume = "13",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Research",

number = "1",

}

Zheng, J, Lin, AY, Huffman, A, Masci, AM, Racz, R, Wu, G, Roan, K, Ong, E, Sarntivijai, S, Hu, J, Asfaw, E, Kahn, H, Li, X, Zhang, X, Monickaraj, J, Kosar, N, Li, J, Manuel, W, Abeysinghe, R, Rehana, H, Bansal, B, Pan, Y, Guo, J, He, V, Song, J, Seleznev, AI, Hur, K, He, A, Davydov, A, Yang, Q, Ostropolets, A, Vita, R, Peters, B, Ruttenberg, A, Diehl, AD, Hoyt, CT, Roncaglia, P, Huntley, RP, Scheuermann, RH, Courtot, M, Todd, T, Sayers, S, Chen, F, Li, X, Yeh, FY, Xiang, Z, Ozgur, A, Whetzel, PL, Musen, MA, Mungall, CJ, Leitner, WW, Cui, L, Colby, LA, Mobley, HLT, Athey, BD, Omenn, GS, Cowell, LG, Tao, C, Hur, J, Smith, B & He, Y 2026, 'VO: The Vaccine Ontology', Scientific Data, vol. 13, no. 1, 994. https://doi.org/10.1038/s41597-026-07298-w

TY - JOUR

T1 - VO

T2 - The Vaccine Ontology

AU - Zheng, Jie

AU - Lin, Asiyah Yu

AU - Huffman, Anthony

AU - Masci, Anna Maria

AU - Racz, Rebecca

AU - Wu, Guanming

AU - Roan, Kallan

AU - Ong, Edison

AU - Sarntivijai, Sirarat

AU - Hu, Joy

AU - Asfaw, Eliyas

AU - Kahn, Hayleigh

AU - Li, Xingxian

AU - Zhang, Xumeng

AU - Monickaraj, Joshua

AU - Kosar, Nilufer

AU - Li, Jianfu

AU - Manuel, Warren

AU - Abeysinghe, Rashmie

AU - Rehana, Hasin

AU - Bansal, Benu

AU - Pan, Yuanyi

AU - Guo, Jinjing

AU - He, Virginia

AU - Song, Justin

AU - Seleznev, Andrey I.

AU - Hur, Katelyn

AU - He, Anna

AU - Davydov, Alexander

AU - Yang, Qi

AU - Ostropolets, Anna

AU - Vita, Randi

AU - Peters, Bjoern

AU - Ruttenberg, Alan

AU - Diehl, Alexander D.

AU - Hoyt, Charles Tapley

AU - Roncaglia, Paola

AU - Huntley, Rachael P.

AU - Scheuermann, Richard H.

AU - Courtot, Melanie

AU - Todd, Thomas

AU - Sayers, Samantha

AU - Chen, Fang

AU - Li, Xinna

AU - Yeh, Feng Yu

AU - Xiang, Zuoshuang

AU - Ozgur, Arzucan

AU - Whetzel, Patricia L.

AU - Musen, Mark A.

AU - Mungall, Christopher J.

AU - Leitner, Wolfgang W.

AU - Cui, Licong

AU - Colby, Lesley A.

AU - Mobley, Harry L.T.

AU - Athey, Brian D.

AU - Omenn, Gilbert S.

AU - Cowell, Lindsay G.

AU - Tao, Cui

AU - Hur, Junguk

AU - Smith, Barry

AU - He, Yongqun

PY - 2026/12

Y1 - 2026/12

N2 - Vaccines are widely used in both research and clinical settings. To facilitate FAIR data practices, we urgently 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 ontologically models 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. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). VO enables semantic queries on vaccine data. It has been shown to enhance the analysis of experimental and clinical vaccine datasets, as well as vaccine-related literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.

AB - Vaccines are widely used in both research and clinical settings. To facilitate FAIR data practices, we urgently 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 ontologically models 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. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). VO enables semantic queries on vaccine data. It has been shown to enhance the analysis of experimental and clinical vaccine datasets, as well as vaccine-related literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.

UR - https://www.scopus.com/pages/publications/105043941880

U2 - 10.1038/s41597-026-07298-w

DO - 10.1038/s41597-026-07298-w

M3 - Article

C2 - 42062309

AN - SCOPUS:105043941880

SN - 2052-4463

VL - 13

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 994

ER -

VO: The Vaccine Ontology

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