title: Updates on the web-based VIOLIN vaccine database and analysis system.
abstract: The integrative Vaccine Investigation and Online Information Network (VIOLIN) vaccine research database and analysis system (http://www.violinet.org) curates, stores, analyses and integrates various vaccine-associated research data. Since its first publication in NAR in 2008, significant updates have been made. Starting from 211 vaccines annotated at the end of 2007, VIOLIN now includes over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases (e.g. cancers and allergies). Under the umbrella of VIOLIN, >10 relatively independent programs are developed. For example, Protegen stores over 800 protective antigens experimentally proven valid for vaccine development. VirmugenDB annotated over 200 'virmugens', a term coined by us to represent those virulence factor genes that can be mutated to generate successful live attenuated vaccines. Specific patterns were identified from the genes collected in Protegen and VirmugenDB. VIOLIN also includes Vaxign, the first web-based vaccine candidate prediction program based on reverse vaccinology. VIOLIN collects and analyzes different vaccine components including vaccine adjuvants (Vaxjo) and DNA vaccine plasmids (DNAVaxDB). VIOLIN includes licensed human vaccines (Huvax) and veterinary vaccines (Vevax). The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines.
authors.affiliation: Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA, Division of Comparative Medicine, University of South Florida, Tampa, FL 33612, USA, Department of Neurology, University of Michigan, 48109, Ann Arbor, MI, USA, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Yongqun
authors.initials: Y
authors.lastname: He
authors.forename: Rebecca
authors.initials: R
authors.lastname: Racz
authors.forename: Samantha
authors.initials: S
authors.lastname: Sayers
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.forename: Thomas
authors.initials: T
authors.lastname: Todd
authors.forename: Junguk
authors.initials: J
authors.lastname: Hur
authors.forename: Xinna
authors.initials: X
authors.lastname: Li
authors.forename: Mukti
authors.initials: M
authors.lastname: Patel
authors.forename: Boyang
authors.initials: B
authors.lastname: Zhao
authors.forename: Monica
authors.initials: M
authors.lastname: Chung
authors.forename: Joseph
authors.initials: J
authors.lastname: Ostrow
authors.forename: Andrew
authors.initials: A
authors.lastname: Sylora
authors.forename: Priya
authors.initials: P
authors.lastname: Dungarani
authors.forename: Guerlain
authors.initials: G
authors.lastname: Ulysse
authors.forename: Kanika
authors.initials: K
authors.lastname: Kochhar
authors.forename: Boris
authors.initials: B
authors.lastname: Vidri
authors.forename: Kelsey
authors.initials: K
authors.lastname: Strait
authors.forename: George W
authors.initials: GW
authors.lastname: Jourdian
authors.forename: Zuoshuang
authors.initials: Z
authors.lastname: Xiang
mesh_terms: D000276:Adjuvants, Immunologic; D000941:Antigens / Q000737:chemistry / Q000235:genetics; D057225:Data Mining; D030541:Databases, Genetic; D005796:Genes; D023281:Genomics; D006801:Humans; D020407:Internet; D010957:Plasmids / Q000235:genetics; D011506:Proteins / Q000276:immunology; D016415:Sequence Alignment; D012984:Software; D018511:Systems Integration; D014612:Vaccines / Q000009:adverse effects / Q000737:chemistry / Q000235:genetics / Q000276:immunology*; D014613:Vaccines, Attenuated / Q000235:genetics; D019444:Vaccines, DNA / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics / Q000276:immunology
chemical_list: D000276:Adjuvants, Immunologic; D000941:Antigens; D011506:Proteins; D014612:Vaccines; D014613:Vaccines, Attenuated; D019444:Vaccines, DNA; D037521:Virulence Factors