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

Overview of computational vaccinology: vaccine development through information technology

“…In addition, it allows the user to perform various simple and advanced searches to retrieve vaccine information (Xiang et al 2008). The Web-based vaccine prediction tool, VaxiJen, is the first server for alignment-independent prediction of protective antigens and subunit vaccines, which is based on auto cross covariance (ACC) transformation of protein sequences into uniform vectors of principal amino acid properties.…”

Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery

“…In essence, the approach consists in two main steps. First, protective antigens (PAs) so far identified in bacterial pathogens are retrieved from the literature (see supplemental References) and from existing database (19) and subjected to bioinformatics analysis in search of common protective signatures (PS) using Blast, ClustalW, Smart, and Pfam (12,13,14,15). Second, PS are launched against the conserved pan-genome of the pathogen of interest with the aim at identifying proteins that share some of the signatures identified by Protectome analysis.…”

dbDiarrhea: The database of pathogen proteins and vaccine antigens from diarrheal pathogens

“…The modules V, VI and VII entail the studies describing (1) vaccine trials for whole organism as well as subunit vaccines. These vaccine candidates are also compared with the other vaccine databases such as VIOLIN (Xiang et al, 2008) and it was found that many candidate strains such as SC599, WRSS1, WRSs2, and WRSs3 from Shigella sp. and 116E, MMU 18,006 from Rotavirus and many more are present in dbDiarhea but untouched in VIOLIN and also VIOLIN doesn't cover the pathogens like Clostridium difficile and Norovirus which are the part of dbDiarrhea.…”