{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T14:01:36Z","timestamp":1722780096871},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2013,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n Licensed human vaccines can induce various adverse events (AE) in vaccinated patients. Due to the involvement of the whole immune system and complex immunological reactions after vaccination, it is difficult to identify the relations among vaccines, adverse events, and human populations in different age groups. Many known vaccine adverse events (VAEs) have been recorded in the package inserts of US-licensed commercial vaccine products. To better represent and analyze VAEs, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Like OAE and VO, OVAE is aligned with the Basic Formal Ontology (BFO). The commercial vaccines and adverse events in OVAE are imported from VO and OAE, respectively. A new population term \u2018human vaccinee population\u2019 is generated and used to define VAE occurrence. An OVAE design pattern is developed to link vaccine, adverse event, vaccinee population, age range, and VAE occurrence. OVAE has been used to represent and classify the adverse events recorded in package insert documents of commercial vaccines licensed by the USA Food and Drug Administration (FDA). OVAE currently includes over 1,300 terms, including 87 distinct types of VAEs associated with 63 human vaccines licensed in the USA. For each vaccine, occurrence rates for every VAE in different age groups have been logically represented in OVAE. SPARQL scripts were developed to query and analyze the OVAE knowledge base data. To demonstrate the usage of OVAE, the top 10 vaccines accompanying with the highest numbers of VAEs and the top 10 VAEs most frequently observed among vaccines were identified and analyzed. Asserted and inferred ontology hierarchies classify VAEs in different levels of AE groups. Different VAE occurrences in different age groups were also analyzed.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n The ontology-based data representation and integration using the FDA-approved information from the vaccine package insert documents enables the identification of adverse events from vaccination in relation to predefined parts of the population (age groups) and certain groups of vaccines. The resulting ontology-based VAE knowledge base classifies vaccine-specific VAEs and supports better VAE understanding and future rational AE prevention and treatment.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/2041-1480-4-40","type":"journal-article","created":{"date-parts":[[2013,11,26]],"date-time":"2013-11-26T18:02:29Z","timestamp":1385488949000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines"],"prefix":"10.1186","volume":"4","author":[{"given":"Erica","family":"Marcos","sequence":"first","affiliation":[]},{"given":"Bin","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,11,26]]},"reference":[{"key":"150_CR1","first-page":"853083","volume":"2013","author":"MP Cunha","year":"2013","unstructured":"Cunha MP, Dorea JG, Marques RC, Leao RS: Vaccine adverse events reported during the first ten years (1998\u20132008) after introduction in the State of Rondonia, Brazil. Biomed Res Int. 2013, 2013: 853083-","journal-title":"Biomed Res Int"},{"key":"150_CR2","first-page":"309","volume-title":"AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), July 26\u201330, 2011","author":"Y He","year":"2011","unstructured":"He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W: Proceeding of ICBO-2011. AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), July 26\u201330, 2011. 2011, NY: University at Buffalo, 309-315."},{"issue":"11","key":"150_CR3","doi-asserted-by":"publisher","first-page":"e49941","DOI":"10.1371\/journal.pone.0049941","volume":"7","author":"S Sarntivijai","year":"2012","unstructured":"Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y: Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS One. 2012, 7 (11): e49941-10.1371\/journal.pone.0049941.","journal-title":"PLoS One"},{"key":"150_CR4","doi-asserted-by":"crossref","unstructured":"He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, et al: The 1st International Conference on Biomedical Ontology (ICBO 2009): July 24\u201326 2009; Buffalo, NY, USA. VO: Vaccine Ontology. Nature Precedings: http:\/\/precedings.nature.com\/documents\/3552\/version\/1","DOI":"10.1038\/npre.2009.3553"},{"issue":"1","key":"150_CR5","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/2041-1480-3-17","volume":"3","author":"Y Lin","year":"2012","unstructured":"Lin Y, He Y: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. J Biomed Semantics. 2012, 3 (1): 17-10.1186\/2041-1480-3-17.","journal-title":"J Biomed Semantics"},{"issue":"11","key":"150_CR6","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25 (11): 1251-1255. 10.1038\/nbt1346.","journal-title":"Nat Biotechnol"},{"issue":"3","key":"150_CR7","doi-asserted-by":"publisher","first-page":"145","DOI":"10.2165\/00002018-200326030-00002","volume":"26","author":"EG Brown","year":"2003","unstructured":"Brown EG: Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA). Drug Saf. 2003, 26 (3): 145-158. 10.2165\/00002018-200326030-00002.","journal-title":"Drug Saf"},{"issue":"4","key":"150_CR8","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1097\/00006454-200404000-00002","volume":"23","author":"F Varricchio","year":"2004","unstructured":"Varricchio F, Iskander J, Destefano F, Ball R, Pless R, Braun MM, Chen RT: Understanding vaccine safety information from the vaccine adverse event reporting system. Pediatr Infect Dis J. 2004, 23 (4): 287-294. 10.1097\/00006454-200404000-00002.","journal-title":"Pediatr Infect Dis J"},{"key":"150_CR9","unstructured":"U.S. Food and Drug Administration: Vaccines Licensed for Immunization and Distribution in the US with Supporting Documents. URL: http:\/\/www.fda.gov\/BiologicsBloodVaccines\/Vaccines\/ApprovedProducts\/UCM093830.htm, accessed on April 3, 2013"},{"issue":"Suppl 21","key":"150_CR10","first-page":"S27","volume":"21","author":"RR Brinkman","year":"2010","unstructured":"Brinkman RR, Courtot M, Derom D, Fostel J, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, et al: Modeling biomedical experimental processes with OBI; June 22. J Biomed Sci. 2010, 21 (Suppl 21): S27-doi:10.1186\/2041-1480-1181-S1181-S1187","journal-title":"J Biomed Sci"},{"key":"150_CR11","unstructured":"PATO: Phenotypic quality ontology. http:\/\/obofoundry.org\/wiki\/index.php\/PATO:Main_Page,"},{"key":"150_CR12","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/1756-0500-3-175","volume":"3","author":"Z Xiang","year":"2010","unstructured":"Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y: OntoFox: web-based support for ontology reuse. BMC Res Notes. 2010, 3: 175-10.1186\/1756-0500-3-175.","journal-title":"BMC Res Notes"},{"key":"150_CR13","volume-title":"SPARQL 1.1 Query Language, W3C Recommendation 21 March 2013","author":"S Harris","year":"2013","unstructured":"Harris S, Seaborne A: SPARQL 1.1 Query Language, W3C Recommendation 21 March 2013. 2013, URL: http:\/\/www.w3.org\/TR\/sparql11-query\/, accessed on August 14, 2013"},{"key":"150_CR14","first-page":"12","volume-title":"Proceedings of the first International Workshop on OWL Reasoner Evaluation (ORE-2012): July 1, 2012","author":"Y Kazakov","year":"2012","unstructured":"Kazakov Y, Kr\u00f6tzsch M, Simanc\u00edk F: ELK reasoner: architecture and evaluation. Proceedings of the first International Workshop on OWL Reasoner Evaluation (ORE-2012): July 1, 2012. 2012, Manchester, UK: CEUR Workshop Proceedings, 12-"},{"issue":"Suppl 2","key":"150_CR15","doi-asserted-by":"publisher","first-page":"S8","DOI":"10.1186\/2041-1480-2-S2-S8","volume":"2","author":"A Ozgur","year":"2011","unstructured":"Ozgur A, Xiang Z, Radev DR, He Y: Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. J Biomed Semantics. 2011, 2 (Suppl 2): S8-10.1186\/2041-1480-2-S2-S8.","journal-title":"J Biomed Semantics"},{"issue":"2","key":"150_CR16","doi-asserted-by":"publisher","first-page":"109","DOI":"10.2165\/00002018-199920020-00002","volume":"20","author":"EG Brown","year":"1999","unstructured":"Brown EG, Wood L, Wood S: The medical dictionary for regulatory activities (MedDRA). Drug Saf. 1999, 20 (2): 109-117. 10.2165\/00002018-199920020-00002.","journal-title":"Drug Saf"},{"key":"150_CR17","volume-title":"Ontorat web server for automatic generation and annotations of new ontology terms","author":"Z Xiang","year":"2012","unstructured":"Xiang Z, Lin Y, He Y: Proceedings of the International Conference on Biomedical Ontologies (ICBO). Ontorat web server for automatic generation and annotations of new ontology terms. 2012, Graz, Austria: University of Graz, July 24\u201327, 2012: URL: http:\/\/ceur-ws.org\/Vol-897\/poster_12.pdf"},{"key":"150_CR18","first-page":"279","volume-title":"Ontobee: A Linked Data Server and Browser for Ontology Terms","author":"Z Xiang","year":"2011","unstructured":"Xiang Z, Mungall C, Ruttenberg A, He Y: Proceedings of the International Conference on Biomedical Ontologies (ICBO). Ontobee: A Linked Data Server and Browser for Ontology Terms. 2011, NY: University at Buffalo, 279-281."},{"issue":"Database issue","key":"150_CR19","first-page":"D923","volume":"36","author":"Z Xiang","year":"2008","unstructured":"Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, et al: VIOLIN: vaccine investigation and online information network. Nucleic Acids Res. 2008, 36 (Database issue): D923-928.","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/2041-1480-4-40.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:18:45Z","timestamp":1630549125000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/2041-1480-4-40"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,26]]},"references-count":19,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["150"],"URL":"https:\/\/doi.org\/10.1186\/2041-1480-4-40","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,26]]},"assertion":[{"value":"17 August 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 November 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 November 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"40"}}