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It is hypothesized that the application of VO will enhance the prediction of IFN-\u03b3 and vaccine-mediated gene interaction network.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, 186 specific vaccine names listed in the Vaccine Ontology (VO) and their semantic relations were used for possible improved retrieval of the IFN-\u03b3 and vaccine associated gene interactions. The application of VO allows discovery of 38 more genes and 60 more interactions. Comparison of different layers of IFN-\u03b3 networks and the example BCG vaccine-induced subnetwork led to generation of new hypotheses. By analyzing all discovered genes using centrality metrics, 32 genes were ranked high in the VO-based IFN-\u03b3 vaccine network using four centrality scores. Furthermore, 28 specific vaccines were found to be associated with these top 32 genes. These specific vaccine-gene associations were further used to generate a network of vaccine-vaccine associations. The BCG and LVS vaccines are found to be the most central vaccines in the vaccine-vaccine association network.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our results demonstrate that the combined usages of biomedical ontologies and centrality-based literature mining are able to significantly facilitate discovery of gene interaction networks and gene-concept associations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>\n                      VO is available at:\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.violinet.org\/vaccineontology\" ext-link-type=\"uri\">http:\/\/www.violinet.org\/vaccineontology<\/jats:ext-link>\n                      ; and the SVM edit kernel for gene interaction extraction is available at:\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.violinet.org\/ifngvonet\/int_ext_svm.zip\" ext-link-type=\"uri\">http:\/\/www.violinet.org\/ifngvonet\/int_ext_svm.zip<\/jats:ext-link>\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/2041-1480-2-s2-s8","type":"journal-article","created":{"date-parts":[[2011,5,19]],"date-time":"2011-05-19T02:17:24Z","timestamp":1305771444000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Mining of vaccine-associated IFN-\u03b3 gene interaction networks using the Vaccine Ontology"],"prefix":"10.1186","volume":"2","author":[{"given":"Arzucan","family":"\u00d6zg\u00fcr","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuoshuang","family":"Xiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dragomir R","family":"Radev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,5,17]]},"reference":[{"issue":"2","key":"34_CR1","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.cytogfr.2009.02.004","volume":"20","author":"A Billiau","year":"2009","unstructured":"Billiau A, Matthys P: Interferon-gamma: a historical perspective. 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