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Ontologies support data standardization and exchange and provide a basis for computer-assisted automated reasoning. IDOBRU is an ontology in the domain of\n                      <jats:italic>Brucella<\/jats:italic>\n                      and brucellosis.\n                      <jats:italic>Brucella<\/jats:italic>\n                      is a Gram-negative intracellular bacterium that causes brucellosis, the most common zoonotic disease in the world. In this study, IDOBRU is used as a platform to model and analyze how the hosts, especially host macrophages, interact with virulent\n                      <jats:italic>Brucella<\/jats:italic>\n                      strains or live attenuated\n                      <jats:italic>Brucella<\/jats:italic>\n                      vaccine strains. Such a study allows us to better integrate and understand intricate\n                      <jats:italic>Brucella<\/jats:italic>\n                      pathogenesis and host immunity mechanisms.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Different levels of host-\n                      <jats:italic>Brucella<\/jats:italic>\n                      interactions based on different host cell types and\n                      <jats:italic>Brucella<\/jats:italic>\n                      strains were first defined ontologically. Three important processes of virulent\n                      <jats:italic>Brucella<\/jats:italic>\n                      interacting with host macrophages were represented:\n                      <jats:italic>Brucella<\/jats:italic>\n                      entry into macrophage, intracellular trafficking, and intracellular replication. Two\n                      <jats:italic>Brucella<\/jats:italic>\n                      pathogenesis mechanisms were ontologically represented:\n                      <jats:italic>Brucella<\/jats:italic>\n                      Type IV secretion system that supports intracellular trafficking and replication, and\n                      <jats:italic>Brucella<\/jats:italic>\n                      erythritol metabolism that participates in\n                      <jats:italic>Brucella<\/jats:italic>\n                      intracellular survival and pathogenesis. The host cell death pathway is critical to the outcome of host-\n                      <jats:italic>Brucella<\/jats:italic>\n                      interactions. For better survival and replication, virulent\n                      <jats:italic>Brucella<\/jats:italic>\n                      prevents macrophage cell death. However, live attenuated\n                      <jats:italic>B. abortus<\/jats:italic>\n                      vaccine strain RB51 induces caspase-2-mediated proinflammatory cell death.\n                      <jats:italic>Brucella<\/jats:italic>\n                      -associated cell death processes are represented in IDOBRU. The gene and protein information of 432 manually annotated\n                      <jats:italic>Brucella<\/jats:italic>\n                      virulence factors were represented using the Ontology of Genes and Genomes (OGG) and Protein Ontology (PRO), respectively. Seven inference rules were defined to capture the knowledge of host-\n                      <jats:italic>Brucella<\/jats:italic>\n                      interactions and implemented in IDOBRU. Current IDOBRU includes 3611 ontology terms. SPARQL queries identified many results that are critical to the host-\n                      <jats:italic>Brucella<\/jats:italic>\n                      interactions. For example, out of 269 protein virulence factors related to macrophage-\n                      <jats:italic>Brucella<\/jats:italic>\n                      interactions, 81 are critical to\n                      <jats:italic>Brucella<\/jats:italic>\n                      intracellular replication inside macrophages. A SPARQL query also identified 11 biological processes important for\n                      <jats:italic>Brucella<\/jats:italic>\n                      virulence.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      To systematically represent and analyze fundamental host-pathogen interaction mechanisms, we provided for the first time comprehensive ontological modeling of host-pathogen interactions using\n                      <jats:italic>Brucella<\/jats:italic>\n                      as the pathogen model. The methods and ontology representations used in our study are generic and can be broadened to study the interactions between hosts and other pathogens.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-015-0036-y","type":"journal-article","created":{"date-parts":[[2015,10,5]],"date-time":"2015-10-05T06:55:09Z","timestamp":1444028109000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Ontology-based representation and analysis of host-Brucella interactions"],"prefix":"10.1186","volume":"6","author":[{"given":"Yu","family":"Lin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuoshuang","family":"Xiang","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":[[2015,10,5]]},"reference":[{"issue":"2","key":"36_CR1","doi-asserted-by":"publisher","first-page":"213","DOI":"10.3201\/eid0302.970219","volume":"3","author":"MJ Corbel","year":"1997","unstructured":"Corbel MJ. 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