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Welcome to VIOLIN!

Infectious diseases remain among the most common and fatal diseases. According to estimations of the World Health Organization, infectious diseases caused 14.7 million deaths in 2001, accounting for 26% of the total global mortality. Vaccines are used to stimulate the immune system to protect against infectious pathogenic microorganisms such as bacteria and viruses. Since the introduction of Edward Jenner’s cowpox vaccine to prevent smallpox in 1796, vaccination has proven a successful means against many infectious diseases. Unfortunately, vaccination against medically important viruses (e.g., Human Immunodeficiency Virus), bacteria (e.g., Mycobacterium tuberculosis), and parasites (e.g, Plasmodium falciparum) has been unsuccessful. These pathogens employ unusual mechanisms that interfere with the host immune response.

A large body of vaccine research and development has been conducted in past decades. Vaccine development has undergone a renaissance in recent years. This is partly attributable to the cost-effectiveness of vaccines and advanced post-genomic technologies. These factors have resulted in appearance of a large number of products and vaccine candidates. There now exists an urgent need for storage, annotation, comparison, and analysis of vaccine information for different pathogens in different hosts. Although various vaccine databases, e.g., the Vaccine Page: http://www.vaccines.org/, exist that list commercialized vaccines and their usages, no web-based central data repository is available to store and analyze research data for commercial vaccines and vaccines in clinical trials or in early stages of research.

Vaccine Investigation and Online Information Network (VIOLIN) is a web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety. The vaccine data includes research data from vaccine studies using humans, natural and laboratory animals.

VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several powerful literature searching and data mining programs have been developed. These include an advanced keywords search program, a natural languagae processing (NLP) based literature retrieval program, a MeSH-based literature browser, and a literature alert program. Registered users can subscribe to our email alert service and will be notified of any newly published vaccine papers in the areas of interest. These literature mining programs are designed to help the user and VIOLIN database curators to find efficiently needed vaccine articles and sentences within full-text articles that contain searched keywords or categories.

A web-based literature mining and curation system (Limix) is available for registered users/curators to search, curate, and submit structured vaccine data into the VIOLIN database. The curated vaccine-related information contains many categories such as general pathogenesis, protective immunity, vaccine preparation and characteristics, host responses including vaccination protocol and efficacy against virulent pathogen infections. All data within the database is edited manually and is derived primarily from peer-reviewed publications. The curated data is stored in a relational database and can be queried using various VIOLIN search programs. Vaccine-related pathogen and host genes are annotated and available for searchs based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.

VIOLIN is designed to be a vital source of vaccine information and will provide researchers in basic and clinical sciences with curated data and bioinformatics tools to facilitate understanding and development of vaccines to fight infectious diseases.