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Welcome to VIOLIN!As illustrated by COVID-19, infectious diseases remain among the most common and fatal diseases throughout the world, contributing to over a quarter of global mortality. Since the introduction of Edward Jenner’s cowpox vaccine to prevent smallpox in 1796, vaccination has proven to be one of the most signficant inventions in modern medicine. While overall very successful, vaccination against many medically important viruses (e.g., Human Immunodeficiency Virus), bacteria (e.g., Mycobacterium tuberculosis), and parasites (e.g, Plasmodium falciparum) are still unsuccessful. Meanwhile, we are facing the challenges to quickly deliver effective and safe vaccines aganist many emerging infectious diseases, such as the COVID-19. New technologies are also being developed to invent vaccines against non-infectious diseases such as cancers and autoimmune diseases. The 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. Although various vaccine resources, such as FDA vaccines, CDC/FDA vaccine adverse event reporting system (VAERS), and the Vaccine Page (http://www.vaccines.org/), exist, these resources focus on commercialized vaccines and their usages. VIOLIN is unique in that it is the comprehensive vaccine resource with a strong focus on vaccine research and analysis. The following figure illustrates major components in our VIOLIN resource:
(Note: The above figure does not include all the components available in VIOLIN.) Here is an introduction of the VIOLIN components:
VIOLIN annotates, 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. The VIOLIN team also leads and maintains the development of the community-based Vaccine Ontology (VO), which has now become an essential computer-interpretable vaccine standard that supports FAIR vaccien data and knowledge standardization, integration, sharing, and analysis. Furthermore, we have developed tools to support vaccine design. We have developed Vaxign, the first web-based vaccine design tool based on the strategy of reverse vaccinology. We have also developed Vaxign-ML, a new machine learning based vaccine antigen prediction tool. These tools have been applied by us and others to design and analyze vaccine candidates against various diseases, including COVID-19. 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.
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