Olsen Lars Rønn, Zhang Guang Lan, Reinherz Ellis L, Brusic Vladimir
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.
Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
Immunome Res. 2011;7(3).
The 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.
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/
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.
该属异常庞大，包含70多个物种，其中一半以上是已知的人类病原体。它包括一组临床相关的感染因子，如登革热、西尼罗河病毒、黄热病和日本脑炎病毒。尽管对这些病原体已进行了广泛研究，但大多数黄病毒仍缺乏安全有效的疫苗。
我们构建了一个数据库，该数据库整合了黄病毒的抗原数据、专门的分析工具以及用于自动复杂分析的工作流程，重点应用于免疫学和疫苗学。FLAVIdB包含12858条黄病毒抗原序列条目、184个经过验证的T细胞表位、201个经过验证的B细胞表位以及登革热病毒包膜蛋白的4个代表性分子结构。FLAVIdB是通过收集、注释和整合来自GenBank、GenPept、UniProt、IEDB和PDB的数据组装而成。这些数据经过了广泛的质量控制（消除冗余、检测错误和统一词汇）。通过整理从文献中提取的信息，对选定的功能相关特征进行了进一步注释。该数据库被纳入一个可通过网络访问的数据挖掘系统，该系统结合了专门的数据分析工具，用于对相关数据类别（蛋白质序列、大分子结构和免疫表位）进行综合分析。该数据挖掘系统包括用于变异性和保守性分析、T细胞表位预测以及B细胞表位中和成分表征的工具。可通过cvc.dfci.harvard.edu/flavi/访问FLAVIdB。
FLAVIdB代表了新一代数据库，其中数据和工具被整合到一个专门设计的数据挖掘基础设施中，旨在通过发现疫苗靶点来辅助合理的疫苗设计。
