- VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on. [PMID: 26578559]
Lihong Chen, Dandan Zheng, Bo Liu, Jian Yang, Qi Jin
Nucleic acids research 2016:44(D1)
32 Citations (Google Scholar as of 2017-05-10)
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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
- VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. [PMID: 22067448]
Lihong Chen, Zhaohui Xiong, Lilian Sun, Jian Yang, Qi Jin
Nucleic acids research 2012:40(Database issue)
140 Citations (Google Scholar as of 2016-01-13)
Abstract: The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has served as a comprehensive repository of bacterial virulence factors (VFs) for >7 years. Bacterial virulence is an exciting and dynamic field, due to the availability of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes. The intricacy of virulence mechanisms offers a challenge, and there exists a clear need to decipher the 'language' used by VFs more effectively. In this article, we present the recent major updates of VFDB in an attempt to summarize some of the most important virulence mechanisms by comparing different compositions and organizations of VFs from various bacterial pathogens, identifying core components and phylogenetic clades and shedding new light on the forces that shape the evolutionary history of bacterial pathogenesis. In addition, the 2012 release of VFDB provides an improved user interface.
- VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. [PMID: 17984080]
Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, Qi Jin
Nucleic acids research 2008:36(Database issue)
109 Citations (Google Scholar as of 2016-01-13)
Abstract: Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which makes comparative genomics a powerful approach for uncovering novel virulence determinants and hidden aspects of pathogenesis. VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization. The VFDB 2008 release includes the following new features; (i) detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus, (ii) multiple alignments and statistical analysis of homologous VFs and (iii) graphical comparison of genomic organizations of virulence genes. Comparative analysis of the numerous VFs will improve our understanding of the nature and evolution of virulence, as well as the development of new therapeutic and preventive strategies. VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/.
- VFDB: a reference database for bacterial virulence factors. [PMID: 15608208]
Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin
Nucleic acids research 2005:33(Database issue)
167 Citations (Google Scholar as of 2016-01-14)
Abstract: Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the mechanisms of the disease processes at the molecular level over the last decades. To facilitate future research, it becomes necessary to form a database collectively presenting the virulence factors (VFs) of various medical significant bacterial pathogens. The aim of virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) is to provide such a source for scientists to rapidly access to current knowledge about VFs from various bacterial pathogens. VFDB is comprehensive and user-friendly. One can search VFDB by browsing each genus or by typing keywords. Furthermore, a BLAST search tool against all known VF-related genes is also available. VFDB provides a unified gateway to store, search, retrieve and update information about VFs from various bacterial pathogens.