Vaccine Investigation and Online Information Network (VIOLIN)

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract Vaccine Investigation and Online Information Network (VIOLIN) is a web-based vaccine database and analysis system.

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

VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several advanced literature searching and data mining programs have been developed.

These include an advanced keywords search program; a natural language processing (NLP) based literature retrieval program, a MeSH- based literature browser, and a literature alert program.

Registered users can subscribe to the manufacturer's 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 searches based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.

Summary of VIOLIN Technologies and Systems:

1) Vaccine Ontology (VO): Dr. Yongqun "Oliver" He (VIOLIN) has initiated and led a community effort to develop the Vaccine Ontology (VO) for vaccine data standardization and analysis, literature mining, and automated reasoning.

VO is being developed through collaborations with Dr. Barry Smith (University at Buffalo and the National Center for Biomedical Ontology), Dr. Lindsay Cowell (Duke University and the Infectious Disease Ontology), Dr. Harry Mobley (University of Michigan), and many other vaccine and ontology experts.

2) Vaccine literature mining: VIOLIN provides several 'literature mining' tools, including natural language processing (NLP)-based Vaxpresso, MeSH-based Vaxmesh, Vaccine alert system Vaxlert, and general vaccine literature search system Litesearch.

Vaxpresso is a Textpresso-powered vaccine literature mining program. It contains all vaccine-related papers on selected pathogens extracted from PubMed. The natural language processing (NLP) and ontology- based Textpresso (see G6G Abstract Number 20254) is then used to process the literature data.

Vomine is in the process of being developed into a vaccine-specific natural language processing (NLP)-based literature mining program using the Vaccine Ontology (VO), Gene Ontology (GO), Medical Subject Headings (MeSH), and other ontology or controlled vocabulary systems.

Vomine is being developed by VIOLIN through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI).

3) Vaccine & vaccine components: Manually curated vaccine data can be queried and analyzed using the manufacturer's Vaxquery search engine.

Vaccine-related genes can be queried with Vaxgen and analyzed using a customized BLAST search program. The manufacturers also include information on vaccine adjuvants (Vaxjo) and vaccine vectors (Vaxvec).

4) Vaccine Mechanisms: The mechanisms of how vaccines work against various diseases are the topics of Vaxism.

Vaxmod specifically targets the study of different animal models used in vaccine R & D.

The manufacturer also plans to build a Vaxnet program which will analyze vaccine-induced response networks using ontology-based information integration, NLP-based literature mining, and other statistical techniques.

5) Vaxign (beta): A new vaccine target design program is available for public use.

Vaxign (Vaccine Design) is a vaccine target prediction and analysis system based on the principle of reverse vaccinology.

Two programs exist in Vaxign: (1) Vaxign Query: provides pre-computed Vaxign results for users to explore, and (2) Dynamic Vaxign Analysis: allows sequence input and dynamic Vaxign execution and result visualization.

6) Vaccine Society: The manufacturer has built several web programs to cover various aspects of the Vaccine Society, including vaccine R & D experts (Vaxperts), vaccine information targeting the public (VaxPub), vaccine companies (VaxCom), vaccine-related regulations (VaxLaw), vaccine media (VaxMedia), vaccine meetings (VaxMeet), vaccine funding and grants (VaxFund), vaccine R & D career opportunities (VaxCareer), and a wiki system for vaccine R & D (Vaccine Wiki).

7) Data Download and Exchange: The curated vaccine data in VIOLIN can be downloaded through an XML-based VIOLIN data format VIOLINML or via a web service called V-Utilities.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site VIOLIN

Price Contact manufacturer.

G6G Abstract Number 20411

G6G Manufacturer Number 104041