): Since the introduction of Edward Jenner's smallpox vaccine in 1796, vaccines have proven invaluable for their ability to stimulate the immune system and to confer protection against pathogenic organisms. Progress in modern vaccine research has been accompanied by a dramatic increase in the number of vaccine-related papers in the published literature. It has become increasingly challenging to identify and annotate vaccine data from this large and diverse literature which no one scientist or team can fully master. Although vaccine databases exist that emphasize commercialized vaccines, no public central repository is available to store research data concerning commercial vaccines, vaccines in clinical trials, or vaccine candidates in early stages of development, in a fashion that render such data available for advanced analyses. To fill this need, we have developed VIOLIN (www.violinet.org), a web-based database system for annotation, storage, and analysis of published vaccine data. An ontology represents consensus-based controlled vocabularies of terms and relations, with associated definitions which are logically formulated in such a way as to promote automated reasoning. A bottleneck of vaccine research and further VIOLIN development is the lack of a vaccine ontology, which in turn makes a significant obstacle for vaccine data standardization, retrieval, integration, and advanced analysis and prediction. Our goal is to develop the community-based Vaccine Ontology (VO) and apply it to efficient vaccine literature mining and analysis of protective immune mechanisms. We will focus on two model pathogens: Escherichia coli and Brucella species. This project contains three specific aims: (1) develop a community-based Vaccine Ontology (VO), and apply it to establish a vaccine knowledgebase and to promote vaccine data integration and query through Semantic Web. The VO development will be achieved through collaboration with vaccine researchers, the Infectious Disease Ontology (IDO) Initiative, and the National Center for Biomedical Ontology (NCBO);(2) develop a VO-based natural language processing (NLP) system and apply it for more efficient retrieval of Brucella and E. coli vaccine information, automated annotation of journal articles with VO terms, and VO improvement. This task will be achieved by collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). (3) analyze and predict vaccine targets and protective immune networks attributable to the interactions between host and vaccine. This will be achieved mainly by VO-based literature mining and a novel genome- and literature-based statistical methodology. This project will be implemented by a strong collaborative team and supported from a large user community. The Vaccine Ontology and its applications to literature mining and for studying protective immunity against Brucella spp. and E. coli will lay a strong foundation for further advanced informatics research on vaccines against infectious diseases in the post-genomics and information era.
Vaccines stimulate the immune system and confer protection against pathogenic microorganisms. A bottleneck of vaccine research is the lack of an ontology (consensus- based controlled vocabularies of terms and relations) to ensure consistency of literature curation and support automated reasoning. The goal of this project is to develop a community-based Vaccine Ontology and apply it to vaccine literature mining and analysis of vaccine-induced immune mechanisms.
|He, Yongqun (2014) Ontology-supported research on vaccine efficacy, safety and integrative biological networks. Expert Rev Vaccines 13:825-41|
|He, Yongqun; Racz, Rebecca; Sayers, Samantha et al. (2014) Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res 42:D1124-32|
|Zheng, Jie; Xiang, Zuoshuang; Stoeckert Jr, Christian J et al. (2014) Ontodog: a web-based ontology community view generation tool. Bioinformatics 30:1340-2|
|Racz, Rebecca; Li, Xinna; Patel, Mukti et al. (2014) DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics 15 Suppl 4:S2|
|Todd, Thomas E; Tibi, Omar; Lin, Yu et al. (2013) Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics 14 Suppl 6:S3|
|He, Yongqun; Cao, Zhiwei; De Groot, Anne S et al. (2013) Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics 14 Suppl 4:I1|
|Xiang, Zuoshuang; He, Yongqun (2013) Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics 14 Suppl 4:S2|
|He, Yongqun; Xiang, Zuoshuang (2013) Databases and in silico tools for vaccine design. Methods Mol Biol 993:115-27|
|Racz, Rebecca; Chung, Monica; Xiang, Zuoshuang et al. (2013) Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccines. Vaccine 31:797-805|
|Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang et al. (2012) Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. J Biomed Biotechnol 2012:831486|
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