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Biol."],"published-print":{"date-parts":[[2017,12]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The community\u2010based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations in a typical host response to vaccination study. Such a model was then applied to represent and compare three microarray studies of host responses to the yellow fever vaccine YF\u201017D. A literature meta\u2010analysis was then conducted to survey yellow fever vaccine response papers and summarize statistical methods, using OBCS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A general ontological model was developed to identify major components in a typical host response to vaccination. Our ontology modeling of three similar studies identified common and different components which may contribute to varying conclusions. Although these three studies all used the same vaccine, human blood samples, similar sample collection time post vaccination, and microarray assays, statistically differentially expressed genes and associated gene functions differed, likely due to the differences in specific variables (e.g., microarray type and human variations). Our manual annotation of 95 papers in human responses to yellow fever vaccines identified 38 data analysis methods. These statistical methods were consistently represented and classified with OBCS. Eight statistical methods not available in existing ontologies were added to OBCS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods. Our ontology\u2010based meta\u2010analysis showed that different experimental results might be due to different experimental assays and conditions, sample variations, and data analysis methods.<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-017-0122-5","type":"journal-article","created":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T12:46:10Z","timestamp":1511441170000},"page":"291-301","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["The Ontology of Biological and Clinical Statistics (OBCS)\u2010based statistical method standardization and meta\u2010analysis of host responses to yellow fever vaccines"],"prefix":"10.1002","volume":"5","author":[{"given":"Jie","family":"Zheng","sequence":"first","affiliation":[{"name":"<!--1--> Department of Genetics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan","family":"Li","sequence":"additional","affiliation":[{"name":"<!--2--> Health Science Center Shenzhen University Shenzhen 518000 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingzhi","family":"Liu","sequence":"additional","affiliation":[{"name":"<!--3--> Department of Mathematics University of Maryland College Park MD 20742 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"<!--4--> Unit for Laboratory Animal Medicine University of Michigan Medical School Ann Arbor MI 48109 USA"},{"name":"<!--5--> Department of Microbiology and Immunology University of Michigan Medical School Ann Arbor MI 48109 USA"},{"name":"<!--6--> Center for Computational Medicine and Bioinformatics University of Michigan Medical School Ann Arbor MI 48109 USA"},{"name":"<!--7--> Comprehensive Cancer Center University of Michigan Medical School Ann Arbor MI 48109 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2017,12]]},"reference":[{"key":"e_1_2_8_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13326\u2010016\u20100100\u20102"},{"key":"e_1_2_8_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"e_1_2_8_4_2","doi-asserted-by":"publisher","DOI":"10.3233\/SW-2012-0086"},{"key":"e_1_2_8_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw918"},{"key":"e_1_2_8_6_2","doi-asserted-by":"publisher","DOI":"10.4258\/hir.2013.19.4.235"},{"key":"e_1_2_8_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2006.01.003"},{"key":"e_1_2_8_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv011"},{"key":"e_1_2_8_9_2","first-page":"67","article-title":"Biomedical ontologies in action: role in knowledge management, data integration and decision support","author":"Bodenreider O.","year":"2009","journal-title":"Yearb. 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