Updates on the web-based VIOLIN vaccine database and analysis system

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.

[1]  Yu Lin,et al.  Ontorat web server for automatic generation and annotations of new ontology terms , 2012, ICBO.

[2]  Yongqun He,et al.  Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network , 2011, BMC Immunology.

[3]  Yongqun He,et al.  BBP: Brucella genome annotation with literature mining and curation , 2006, BMC Bioinformatics.

[4]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[5]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[6]  Rino Rappuoli,et al.  Reverse vaccinology. , 2000, Current opinion in microbiology.

[7]  Yu Lin,et al.  Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses , 2012, J. Biomed. Semant..

[8]  Bjoern Peters,et al.  Ontology representation and ANOVA analysis of vaccine protection investigation , 2010 .

[9]  Yongqun He,et al.  Protegen: a web-based protective antigen database and analysis system , 2010, Nucleic Acids Res..

[10]  René Ecochard,et al.  Relationship between haemagglutination-inhibiting antibody titres and clinical protection against influenza: development and application of a bayesian random-effects model , 2010, BMC medical research methodology.

[11]  Huajun Chen,et al.  The Semantic Web , 2011, Lecture Notes in Computer Science.

[12]  Yongqun He,et al.  Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN , 2010, Immunome research.

[13]  Gajendra P. S. Raghava,et al.  AntigenDB: an immunoinformatics database of pathogen antigens , 2009, Nucleic Acids Res..

[14]  D. Ussery,et al.  Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets. , 2012, Gene.

[15]  R. Feachem.  Editorial: The Research Imperative: Fighting AIDS, TB and Malaria , 2004, Tropical medicine & international health : TM & IH.

[16]  Werner Ceusters,et al.  AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events , 2011, ICBO.

[17]  Yongqun He,et al.  Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development , 2012, Journal of biomedicine & biotechnology.

[18]  Yongqun He,et al.  Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database , 2012 .

[19]  Yu Lin,et al.  Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates , 2013, BMC Bioinformatics.

[20]  Yongqun He,et al.  Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development , 2010, Journal of biomedicine & biotechnology.

[21]  Bin Zhao,et al.  The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines , 2013, J. Biomed. Semant..

[22]  Tim Berners-Lee,et al.  Linked Data - The Story So Far , 2009, Int. J. Semantic Web Inf. Syst..

[23]  G. Bansal,et al.  Immunogenic and Invasive Properties of Brucella melitensis 16M Outer Membrane Protein Vaccine Candidates Identified via a Reverse Vaccinology Approach , 2013, PloS one.

[24]  Fang Chen,et al.  VIOLIN: vaccine investigation and online information network , 2007, Nucleic Acids Res..

[25]  Rebecca Racz,et al.  DNAVaxDB: the first web-based DNA vaccine database and its data analysis , 2014, BMC Bioinformatics.

[26]  Ryan R Brinkman,et al.  OntoFox: web-based support for ontology reuse , 2010, BMC Research Notes.

[27]  Shuzhao Li,et al.  Systems vaccinology: Probing humanity’s diverse immune systems with vaccines , 2014, Proceedings of the National Academy of Sciences.

[28]  Yongqun He,et al.  Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology , 2013, BMC Bioinformatics.

[29]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[30]  R. Rappuoli.  Reverse vaccinology : Genomics , 2000 .

[31]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[32]  Alan Ruttenberg,et al.  Ontobee: A Linked Data Server and Browser for Ontology Terms , 2011, ICBO.

[33]  Y. He,et al.  Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccines. , 2013, Vaccine.

[34]  Bjoern Peters,et al.  VO: Vaccine Ontology , 2009 .

[35]  L. Wilkinson.  Immunity , 1891, The Lancet.

[36]  A. A. Magalhães,et al.  reannotation of the Corynebacterium diphtheriae ncTc13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria , 2012 .

[37]  G. Omenn,et al.  Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated with Killed and Live Influenza Vaccines , 2012, PloS one.

[38]  Vladimir Brusic,et al.  Computational vaccinology and the ICoVax 2012 workshop , 2013, BMC Bioinformatics.

[39]  Robert T. Chen,et al.  Emerging Vaccine Informatics , 2011, Journal of biomedicine & biotechnology.

[40]  James A. Hendler,et al.  The Semantic Web" in Scientific American , 2001 .

[41]  Dragomir R. Radev,et al.  Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology , 2011, J. Biomed. Semant..

[42]  Shuzhao Li,et al.  Systems vaccinology: learning to compute the behavior of vaccine induced immunity , 2012, Wiley interdisciplinary reviews. Systems biology and medicine.

[43]  Y. He,et al.  Vaxign: a web-based vaccine target design program for reverse vaccinology , 2009 .

[44]  Adam D. Schuyler,et al.  SciMiner: web-based literature mining tool for target identification and functional enrichment analysis , 2009, Bioinform..

[45]  Ankit Gupta,et al.  Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions , 2013, BMC Bioinformatics.

[46]  Christopher B Wilson,et al.  A decade of vaccines: Integrating immunology and vaccinology for rational vaccine design. , 2010, Immunity.