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Facilitating the Analysis of Immunological Data with Visual Analytic Techniques

Facilitating the Analysis of Immunological Data with Visual Analytic Techniques

Published on: January 2, 2011

Updates on the web-based VIOLIN vaccine database and analysis system.

Yongqun He¹, Rebecca Racz, Samantha Sayers

¹Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA, Division of Comparative Medicine, University of South Florida, Tampa, FL 33612, USA, Department of Neurology, University of Michigan, 48109, Ann Arbor, MI, USA, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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Summary

This summary is machine-generated.

The Vaccine Investigation and Online Information Network (VIOLIN) database now contains over 3240 vaccines for infectious and noninfectious diseases. It integrates diverse vaccine research data and tools, aiding vaccine development and analysis.

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Area of Science:

* Bioinformatics
* Immunology
* Vaccinology

Background:

* The Vaccine Investigation and Online Information Network (VIOLIN) is a comprehensive vaccine research database and analysis system.
* Since its inception in 2008, VIOLIN has undergone significant expansion and updates.
* It aims to curate, store, analyze, and integrate diverse vaccine-associated research data.

Purpose of the Study:

* To present the updated VIOLIN database, highlighting its expanded content and integrated analytical tools.
* To showcase the development of specialized programs within VIOLIN for vaccine research.
* To demonstrate the application of standardized ontologies for data integration and analysis.

Main Methods:

* Data curation and integration of vaccine information, including antigens, virulence factors, adjuvants, and DNA plasmids.
* Development and incorporation of specialized modules such as Protegen, VirmugenDB, Vaxign, Vaxjo, and DNAVaxDB.
* Application of the Vaccine Ontology and the Ontology of Vaccine Adverse Events (OVAE) for data standardization and representation.

Main Results:

* VIOLIN now encompasses over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases.
* Protegen contains over 800 protective antigens, and VirmugenDB annotates over 200 'virmugens'.
* Integrated tools like Vaxign facilitate vaccine candidate prediction, and databases cover adjuvants, DNA plasmids, and licensed vaccines (human and veterinary).

Conclusions:

* VIOLIN serves as a valuable, integrated resource for vaccine research, significantly expanding its scope and utility.
* The system's modular design and application of ontologies enhance data standardization, integration, and analysis.
* VIOLIN supports various stages of vaccine development, from candidate prediction to adverse event tracking.