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Vaccine Ontology in VIOLIN

     Since the introduction of Edward Jenner’s cowpox-based vaccine against smallpox in 1796, vaccines have proven invaluable for their ability to stimulate the immune system and for confer protection against pathogenic microorganisms. Vaccine research and development has undergone a renaissance that is in part attributable to the cost-effectiveness of vaccines and to advanced post-genomic technologies. As progress in vaccine research has been accompanied by a dramatic increase in the number of vaccine-related papers, it has become increasingly challenging to identify and annotate vaccine data from literature. There exists an ever increasing need for a means to store, annotate, compare, and analyze vaccine information as this relates to different pathogens and different hosts. Although vaccine databases exist that emphasize commercialized vaccines, no public central repository is available to store research data concerning either commercial vaccines, those vaccines in clinical trials or those in early stages of development, in a way which makes this data available for analysis. To fill this need, we have developed VIOLIN, a web-based database system for annotation, storage, and analysis of published vaccine data (http://www.violinet.org). A bottleneck of vaccine research is the lack of a Vaccine Ontology for vaccine data standardization, integration, and analysis. We propose to create such an ontology in order to ensure consistency of literature curation and to support automated reasoning.

     The Vaccine Ontology will be used in VIOLIN to represent and organize the vaccine data in the VIOLIN vaccine database. A vaccine Semantics Web will be established in VIOLIN based on the ontology. The Vaccine Ontology will also be used to develop an ontology-based natural language processing (NLP) and literature mining system by collaborating with the National Center for Integrative Biomedical Informatics (NCIBI).