title: FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology.
abstract: BACKGROUND
  Theflavivirusgenus 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/
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA ; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Lars Rønn
authors.initials: LR
authors.lastname: Olsen
authors.affiliation: Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Guang Lan
authors.initials: GL
authors.lastname: Zhang
authors.affiliation: Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA ; Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115, USA ; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Ellis L
authors.initials: EL
authors.lastname: Reinherz
authors.affiliation: Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA ; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Brusic