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[Preprint]. 2025 Aug 15:2025.08.12.669998.

doi: 10.1101/2025.08.12.669998.

VO: The Vaccine Ontology

Jie Zheng¹, Asiyah Yu Lin¹, Anthony Huffman¹, Anna Maria Masci², Rebecca Racz¹, Guanming Wu³, Kallan Roan¹, Edison Ong¹, Sirarat Sarntivijai⁴, Joy Hu¹, Eliyas Asfaw¹, Hayleigh Kahn¹, Xingxian Li¹, Xumeng Zhang¹, Nilufer Kosar⁵, Jianfu Li⁶, Warren Manuel⁷, Rashmie Abeysinghe⁷, Hasin Rehana⁸, Benu Bansal⁸, Yuanyi Pan¹, Jinjing Guo¹, Virginia He⁹, Justin Song¹, Andrey I Seleznev¹⁰, Katelyn Hur¹¹, Anna He¹², Alexander Davydov¹³, Qi Yang¹⁴, Randi Vita¹⁵, Bjoern Peters¹⁵, Alan Ruttenberg¹⁶, Alexander D Diehl¹⁶, Charles Tapley Hoyt¹⁷, Paola Roncaglia¹⁸, Rachael P Huntley¹⁸, Richard H Scheuermann¹⁹, Melanie Courtot²⁰, Thomas Todd²¹, Samantha Sayers¹, Fang Chen¹, Xinna Li¹, Feng-Yu Yeh¹, Zuoshuang Xiang¹, Arzucan Ozgur¹, Patricia L Whetzel²², Mark A Musen²³, Christopher J Mungall²⁴, Wolfgang W Leitner²⁵, Licong Cui⁷, Lesley A Colby¹, Harry L T Mobley¹, Brian D Athey¹, Gilbert S Omenn¹, Lindsay G Cowell²⁶, Cui Tao⁶, Junguk Hur⁸, Barry Smith¹⁶, Yongqun He¹

Affiliations

¹ University of Michigan, Ann Arbor, MI, USA.
² University of Texas MD Anderson Cancer Center, Houston, TX, USA.
³ Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, United States.
⁴ IT Research, Development and Medicine, Boehringer Ingelheim GmbH, 88397 Biberach an der Riß, Germany.
⁵ University of Maryland, College Park, MD, USA.
⁶ Mayo Clinic, Jacksonville, FL, USA.
⁷ University of Texas Health Science Center at Houston, Houston, TX, USA.
⁸ University of North Dakota, Grand Forks, ND, USA.
⁹ Brown University, Providence, RI, USA.
¹⁰ University of Pittsburgh, Pittsburgh, PA, USA.
¹¹ Red River High School, Grand Forks, ND, USA.
¹² Huron High School, Ann Arbor, MI, USA.
¹³ Thesaurus Health, New York City, NY, USA.
¹⁴ IQVIA, Inc., Durham, NC, USA.
¹⁵ La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
¹⁶ University at Buffalo, Buffalo, NY, USA.
¹⁷ Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
¹⁸ SciBite from Elsevier, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, UK.
¹⁹ Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
²⁰ Ontario Institute for Cancer Research and University of Toronto, ON, Canada.
²¹ University of Houston, Houston, TX, USA.
²² University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
²³ Stanford University, Stanford, CA, USA.
²⁴ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
²⁵ National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA.
²⁶ UT Southwestern Medical Center, Dallas, Texas, USA.

PMID: 40832256
PMCID: PMC12363946
DOI: 10.1101/2025.08.12.669998

VO: The Vaccine Ontology

Jie Zheng et al. bioRxiv. 2025.

[Preprint]. 2025 Aug 15:2025.08.12.669998.

doi: 10.1101/2025.08.12.669998.

Authors

Affiliations

¹ University of Michigan, Ann Arbor, MI, USA.
² University of Texas MD Anderson Cancer Center, Houston, TX, USA.
³ Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, United States.
⁴ IT Research, Development and Medicine, Boehringer Ingelheim GmbH, 88397 Biberach an der Riß, Germany.
⁵ University of Maryland, College Park, MD, USA.
⁶ Mayo Clinic, Jacksonville, FL, USA.
⁷ University of Texas Health Science Center at Houston, Houston, TX, USA.
⁸ University of North Dakota, Grand Forks, ND, USA.
⁹ Brown University, Providence, RI, USA.
¹⁰ University of Pittsburgh, Pittsburgh, PA, USA.
¹¹ Red River High School, Grand Forks, ND, USA.
¹² Huron High School, Ann Arbor, MI, USA.
¹³ Thesaurus Health, New York City, NY, USA.
¹⁴ IQVIA, Inc., Durham, NC, USA.
¹⁵ La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
¹⁶ University at Buffalo, Buffalo, NY, USA.
¹⁷ Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
¹⁸ SciBite from Elsevier, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, UK.
¹⁹ Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
²⁰ Ontario Institute for Cancer Research and University of Toronto, ON, Canada.
²¹ University of Houston, Houston, TX, USA.
²² University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
²³ Stanford University, Stanford, CA, USA.
²⁴ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
²⁵ National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA.
²⁶ UT Southwestern Medical Center, Dallas, Texas, USA.

PMID: 40832256
PMCID: PMC12363946
DOI: 10.1101/2025.08.12.669998

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.

Keywords: FAIR; Semantic Web; VO; Vaccine Ontology; ontology; vaccination; vaccine.

PubMed Disclaimer

Conflict of interest statement

Competing Interests Dr. Yongqun He (Oliver) is an Editorial Board Member for Scientific Data, and has served as a Guest Editor for the “Data standards and ontologies for clinical and medical research” Collection.

Figures

**Figure 1.. High-level structure of VO.**
(abridged: some intermediate non-VO terms omitted for simplicity)

**Figure 2.**
Representative vaccine types and their associated hierarchies as defined in the VO.

**Figure 3.. VO representation of the LTA1 vaccine adjuvant.**
**(a)** VO representation of the adjuvant, including three immune profiles induced by the adjuvant. **(b)** DL queries constructed from these three ‘immune profiles’ successfully retrieve the LTA1 adjuvant.

**Figure 4.. Vaccine ontology design pattern (ODP) in VO.**
**(a)** ODP of a typical vaccine. **(b)** Illustration of vaccine ODP with ‘Afluria vaccine.’ **(c)** Representation of ‘Afluria vaccine’ in VO with inferred parents highlighted in yellow.

**Figure 5.. Semantic queries for vaccine identification based on vaccine features using DL and SPARQL query methods.**
(a) Find *Brucella* vaccines; (b) Find influenza vaccines licensed for use in chickens; (c) Find vaccines that immunize against *Bordetella pertussis* defined in the OHDSI vocabularies with their IDs assigned by different resources

**Figure 6.. VO terms used in ImmPort.**
**(a)** VO hierarchy of vaccines and adjuvants in ImmPort. **(b)** COVID-19 vaccine terms with number of studies in ImmPort. **(c)** Vaccine adjuvants with number of studies in ImmPort.

See this image and copyright information in PMC

References

1. Delany I., Rappuoli R. & De Gregorio E. Vaccines for the 21st century. EMBO Mol Med 6, 708–720, 10.1002/emmm.201403876 (2014). - DOI - PMC - PubMed
1. Rodrigues C. M. C. & Plotkin S. A. Impact of Vaccines; Health, Economic and Social Perspectives. Front Microbiol 11, 1526, 10.3389/fmicb.2020.01526 (2020). - DOI - PMC - PubMed
1. Watson O. J. et al. Global impact of the first year of COVID-19 vaccination: a mathematical modelling study. Lancet Infect Dis 22, 1293–1302, 10.1016/S1473-3099(22)00320-6 (2022). - DOI - PMC - PubMed
1. Centers for Disease Control and Prevention. CVX (Vaccine Administered), https://www2.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx (2024).
1. U.S. Food and Drug Administration. FDA Approved Vaccines, https://www.fda.gov/vaccines-blood-biologics/vaccines/vaccines-licensed-... (2025).

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This is a preprint.

VO: The Vaccine Ontology

Affiliations

VO: The Vaccine Ontology

Authors

Affiliations

Abstract

Conflict of interest statement

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