VIOLIN: vaccine investigation and online information network

Abstract

Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

Figure 1.

Entity relationship diagram of the VIOLIN database. The details of table reference and user are not shown in this figure. The diamond represents a one-to-many (blank-to-solid) relationship between two tables.

Figure 2.

Example of vaccine search and comparison. A keyword search of ‘superoxide dismutase’ (SOD) in Vaxquery (A) identified five vaccines curated in VIOLIN, including the Brucella abortus DNA vaccine expressing the gene sodC encoding for Cu/Zn superoxide dismutase and M. tuberculosis expressing the gene sodA encoding for Fe superoxide dismutase (B). DNA vaccines against either enzyme have been found to be effective against challenge infections by virulent B. abortus or M. tuberculosis strains (C). However, a VIOLIN BLAST-2-Sequences search did not find significant similarity between these two SOD protein sequences (D).