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VFDB 2022: a general classification scheme for bacterial virulence factors
The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs wi...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728188/ https://www.ncbi.nlm.nih.gov/pubmed/34850947 http://dx.doi.org/10.1093/nar/gkab1107 |
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author | Liu, Bo Zheng, Dandan Zhou, Siyu Chen, Lihong Yang, Jian |
author_facet | Liu, Bo Zheng, Dandan Zhou, Siyu Chen, Lihong Yang, Jian |
author_sort | Liu, Bo |
collection | PubMed |
description | The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide. |
format | Online Article Text |
id | pubmed-8728188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87281882022-01-05 VFDB 2022: a general classification scheme for bacterial virulence factors Liu, Bo Zheng, Dandan Zhou, Siyu Chen, Lihong Yang, Jian Nucleic Acids Res Database Issue The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide. Oxford University Press 2021-11-30 /pmc/articles/PMC8728188/ /pubmed/34850947 http://dx.doi.org/10.1093/nar/gkab1107 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Liu, Bo Zheng, Dandan Zhou, Siyu Chen, Lihong Yang, Jian VFDB 2022: a general classification scheme for bacterial virulence factors |
title | VFDB 2022: a general classification scheme for bacterial virulence factors |
title_full | VFDB 2022: a general classification scheme for bacterial virulence factors |
title_fullStr | VFDB 2022: a general classification scheme for bacterial virulence factors |
title_full_unstemmed | VFDB 2022: a general classification scheme for bacterial virulence factors |
title_short | VFDB 2022: a general classification scheme for bacterial virulence factors |
title_sort | vfdb 2022: a general classification scheme for bacterial virulence factors |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728188/ https://www.ncbi.nlm.nih.gov/pubmed/34850947 http://dx.doi.org/10.1093/nar/gkab1107 |
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