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

By Lihong Chen, Dandan Zheng, Bo Liu, Jian Yang, Qi Jin. Nucleic Acids Res., 2015

1,508 citations recorded by the source corpus.

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.

Subfields: Clinical Biochemistry, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/04163a7e819b37f7ed1c9031ea128132e1465975

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Citations in the corpus

VFDB 2022: a general classification scheme for bacterial virulence factors (2021, background): “Thus, the follow-up in-depth mining of the panbacterial microbiome data in terms of pathogenesis requires a well-organized reference category of all established bacterial VFs from various known pathogens (6).”
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements (2021, methodology): “7 [3]; metal resistance genes were annotated using BacMet [4], and virulence factors were annotated using VF-db [5].”
VFDB 2019: a comparative pathogenomic platform with an interactive web interface (2018, methodology): “By the last release, an alternative JavaScript-based interface was further introduced to present the full contents of the database interactively (13).”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, positive): “VICTORS, the Virulence Factor Database (VFDB) (25) and a separate collection of PATRIC virulence factors (26) are used to identify virulence factors.”
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes (2021, neutral): “…strand (%), proportion of CDS on negative sense strand (%), coding capacity (%), number of transfer-RNAs (tRNAs), bacterial host, viral genus, viral subfamily, viral family, viral realm, Baltimore group (derived from phylum), and the lowest viral taxa available (from genus, subfamily, and family).”