VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on

Abstract

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. Since its inception the VFDB has served as a comprehensive repository of bacterial VFs for over a decade. The exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets--one core dataset of experimentally verified VFs only and another full dataset including all known and predicted VFs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. Our efforts enhanced the data quality of the VFDB and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial VFs.

Figure 1.

Schematic diagram of the relationship between previous releases of virulence factor database (VFDB). R1 forms the base and core of the database, whereas R2 and R3 provided a comparative genomics platform and expanded the data contents in terms of genomes and pathogens (illustrated by the horizontal bars on the top), respectively.