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Many such immune responses have not been thoroughly examined and classified. The Vaccine Ontology (VO) is a community-based ontology in the domain of vaccinology. We here describe how VO is used to represent the variety of immune responses associated with vaccines, together with associated biomarkers and profiles.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The VO differentiates \u2018vaccination\u2019 and \u2018vaccine immunization.\u2019 The former is a process of administering a vaccine in vivo; the latter is the outcome of vaccine induction of immune response. This distinction is critical for understanding both the procedure of vaccination and the resulting immune effects. VO also models and represents various vaccine-induced responses at multiple biological levels, including population, organism, organ\/tissue, cell, and gene\/protein levels. Such an approach captures the complexity of vaccine-induced immunity, from population-wide trend (for example: herd immunity) to molecular mechanisms. VO defines immune biomarkers as material entities such as neutralizing antibodies that signify a humoral immune response, and IFN gamma that is indicative of cell-mediated responses. Such biomarkers provide measurable indicators of the immune system\u2019s functional state post vaccination, enabling robust evaluation of vaccine efficacy. VO classifies \u2018immune response profile\u2019 and \u2018correlated profile (or correlate) of immune protection\u2019 as \u2018process profiles,\u2019 a class in the Basic Formal Ontology (BFO 2.0). Immune response profiles, such as \u2018Th1 (or Th2)-biased profile,\u2019 can be induced by various vaccines and vaccine adjuvants. Different types of \u2018correlated profile of immune protection\u2019 are also identified, such as mechanistic and non-mechanistic correlates of immune protection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The important immune-related terms for immune biomarkers, profiles, and responses are modeled ontologically in VO together with their interrelations. The results support enhanced classification and analysis of vaccine-induced immune responses and related biomarkers and immune profiles, leading to further understanding of the vaccine immune mechanisms and enhanced vaccine research and development.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-026-00360-x","type":"journal-article","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T05:58:06Z","timestamp":1782712686000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Immune biomarkers, profiles, and responses: a vaccine ontology perspective"],"prefix":"10.1186","volume":"17","author":[{"given":"Yongqun","family":"He","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Huffman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Maria","family":"Masci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asiyah Yu","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,27]]},"reference":[{"issue":"4\u20135","key":"360_CR1","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/j.ijmm.2005.12.015","volume":"296","author":"K Becker","year":"2006","unstructured":"Becker K, Hu Y, Biller-Andorno N. 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