title: Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.
abstract: BACKGROUND
  Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets.
  
  
  RESULTS
  VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system.
  
  
  CONCLUSIONS
  Bioinformatics curation and ontological representation of Brucella vaccines promotes classification and analysis of existing Brucella vaccines and vaccine candidates. Computational prediction of Brucella vaccine targets provides more candidates for rational vaccine development. The use of VIOLIN provides a general approach that can be applied for analyses of vaccines against other pathogens and infection diseases.
authors.affiliation: Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. yongqunh@umich.edu.
authors.forename: Yongqun
authors.initials: Y
authors.lastname: He
authors.forename: Zuoshuang
authors.initials: Z
authors.lastname: Xiang