FLAVIdB

A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology

Lars Rønn Olsen, Guang Lan Zhang, Ellis L. Reinherz, Vladimir Brusic

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Background: The flavivirus genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. Results: We have assembled a database that combines antigenic data of flaviviruses, specialized analysis tools, and workflows for automated complex analyses focusing on applications in immunology and vaccinology. FLAVIdB contains 12,858 entries of flavivirus antigen sequences, 184 verified T-cell epitopes, 201 verified B-cell epitopes, and 4 representative molecular structures of the dengue virus envelope protein. FLAVIdB was assembled by collection, annotation, and integration of data from GenBank, GenPept, UniProt, IEDB, and PDB. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). Further annotation of selected functionally relevant features was performed by organizing information extracted from the literature. The database was incorporated into a web-accessible data mining system, combining specialized data analysis tools for integrated analysis of relevant data categories (protein sequences, macromolecular structures, and immune epitopes). The data mining system includes tools for variability and conservation analysis, T-cell epitope prediction, and characterization of neutralizing components of B-cell epitopes. FLAVIdB is accessible at cvc.dfci.harvard.edu/flavi/ Conclusion: FLAVIdB represents a new generation of databases in which data and tools are integrated into a data mining infrastructures specifically designed to aid rational vaccine design by discovery of vaccine targets.

Original languageEnglish
Article number2
JournalImmunome Research
Volume7
Issue number3
Publication statusPublished - 2011
Externally publishedYes

Fingerprint

Immunology
Epitopes
Flavivirus
Data Mining
Knowledge Discovery
Allergy and Immunology
Information Systems
Data mining
Vaccines
Vaccine
B-Lymphocyte Epitopes
T-Lymphocyte Epitopes
Databases
T-cells
B Cells
Pathogens
West Nile Fever
Viruses
Virus
Annotation

ASJC Scopus subject areas

  • Immunology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics
  • Computer Science Applications

Cite this

FLAVIdB : A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. / Olsen, Lars Rønn; Zhang, Guang Lan; Reinherz, Ellis L.; Brusic, Vladimir.

In: Immunome Research, Vol. 7, No. 3, 2, 2011.

Research output: Contribution to journalArticle

Olsen, Lars Rønn ; Zhang, Guang Lan ; Reinherz, Ellis L. ; Brusic, Vladimir. / FLAVIdB : A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. In: Immunome Research. 2011 ; Vol. 7, No. 3.
@article{0f8254022ef34ebca8f51b3de9dd0601,
title = "FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology",
abstract = "Background: The flavivirus genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. Results: We have assembled a database that combines antigenic data of flaviviruses, specialized analysis tools, and workflows for automated complex analyses focusing on applications in immunology and vaccinology. FLAVIdB contains 12,858 entries of flavivirus antigen sequences, 184 verified T-cell epitopes, 201 verified B-cell epitopes, and 4 representative molecular structures of the dengue virus envelope protein. FLAVIdB was assembled by collection, annotation, and integration of data from GenBank, GenPept, UniProt, IEDB, and PDB. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). Further annotation of selected functionally relevant features was performed by organizing information extracted from the literature. The database was incorporated into a web-accessible data mining system, combining specialized data analysis tools for integrated analysis of relevant data categories (protein sequences, macromolecular structures, and immune epitopes). The data mining system includes tools for variability and conservation analysis, T-cell epitope prediction, and characterization of neutralizing components of B-cell epitopes. FLAVIdB is accessible at cvc.dfci.harvard.edu/flavi/ Conclusion: FLAVIdB represents a new generation of databases in which data and tools are integrated into a data mining infrastructures specifically designed to aid rational vaccine design by discovery of vaccine targets.",
author = "Olsen, {Lars R{\o}nn} and Zhang, {Guang Lan} and Reinherz, {Ellis L.} and Vladimir Brusic",
year = "2011",
language = "English",
volume = "7",
journal = "Immunome Research",
issn = "1745-7580",
publisher = "OMICS Publishing Group",
number = "3",

}

TY - JOUR

T1 - FLAVIdB

T2 - A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology

AU - Olsen, Lars Rønn

AU - Zhang, Guang Lan

AU - Reinherz, Ellis L.

AU - Brusic, Vladimir

PY - 2011

Y1 - 2011

N2 - Background: The flavivirus genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. Results: We have assembled a database that combines antigenic data of flaviviruses, specialized analysis tools, and workflows for automated complex analyses focusing on applications in immunology and vaccinology. FLAVIdB contains 12,858 entries of flavivirus antigen sequences, 184 verified T-cell epitopes, 201 verified B-cell epitopes, and 4 representative molecular structures of the dengue virus envelope protein. FLAVIdB was assembled by collection, annotation, and integration of data from GenBank, GenPept, UniProt, IEDB, and PDB. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). Further annotation of selected functionally relevant features was performed by organizing information extracted from the literature. The database was incorporated into a web-accessible data mining system, combining specialized data analysis tools for integrated analysis of relevant data categories (protein sequences, macromolecular structures, and immune epitopes). The data mining system includes tools for variability and conservation analysis, T-cell epitope prediction, and characterization of neutralizing components of B-cell epitopes. FLAVIdB is accessible at cvc.dfci.harvard.edu/flavi/ Conclusion: FLAVIdB represents a new generation of databases in which data and tools are integrated into a data mining infrastructures specifically designed to aid rational vaccine design by discovery of vaccine targets.

AB - Background: The flavivirus genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. Results: We have assembled a database that combines antigenic data of flaviviruses, specialized analysis tools, and workflows for automated complex analyses focusing on applications in immunology and vaccinology. FLAVIdB contains 12,858 entries of flavivirus antigen sequences, 184 verified T-cell epitopes, 201 verified B-cell epitopes, and 4 representative molecular structures of the dengue virus envelope protein. FLAVIdB was assembled by collection, annotation, and integration of data from GenBank, GenPept, UniProt, IEDB, and PDB. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). Further annotation of selected functionally relevant features was performed by organizing information extracted from the literature. The database was incorporated into a web-accessible data mining system, combining specialized data analysis tools for integrated analysis of relevant data categories (protein sequences, macromolecular structures, and immune epitopes). The data mining system includes tools for variability and conservation analysis, T-cell epitope prediction, and characterization of neutralizing components of B-cell epitopes. FLAVIdB is accessible at cvc.dfci.harvard.edu/flavi/ Conclusion: FLAVIdB represents a new generation of databases in which data and tools are integrated into a data mining infrastructures specifically designed to aid rational vaccine design by discovery of vaccine targets.

UR - http://www.scopus.com/inward/record.url?scp=84866977551&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84866977551&partnerID=8YFLogxK

M3 - Article

VL - 7

JO - Immunome Research

JF - Immunome Research

SN - 1745-7580

IS - 3

M1 - 2

ER -