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Curation, integration and visualization of bacterial virulence factors in PATRIC
Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found i...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287947/ https://www.ncbi.nlm.nih.gov/pubmed/25273106 http://dx.doi.org/10.1093/bioinformatics/btu631 |
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author | Mao, Chunhong Abraham, David Wattam, Alice R. Wilson, Meredith J.C. Shukla, Maulik Yoo, Hyun Seung Sobral, Bruno W. |
author_facet | Mao, Chunhong Abraham, David Wattam, Alice R. Wilson, Meredith J.C. Shukla, Maulik Yoo, Hyun Seung Sobral, Bruno W. |
author_sort | Mao, Chunhong |
collection | PubMed |
description | Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity. Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A–C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein–protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC. Availability and implementation: All tools and data are freely available at PATRIC (http://patricbrc.org). Contact: cmao@vbi.vt.edu. Supplementary information: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-4287947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-42879472015-01-30 Curation, integration and visualization of bacterial virulence factors in PATRIC Mao, Chunhong Abraham, David Wattam, Alice R. Wilson, Meredith J.C. Shukla, Maulik Yoo, Hyun Seung Sobral, Bruno W. Bioinformatics Original Papers Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity. Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A–C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein–protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC. Availability and implementation: All tools and data are freely available at PATRIC (http://patricbrc.org). Contact: cmao@vbi.vt.edu. Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2015-01-15 2014-09-30 /pmc/articles/PMC4287947/ /pubmed/25273106 http://dx.doi.org/10.1093/bioinformatics/btu631 Text en © The Author 2014. Published by Oxford University Press. All rights reserved http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Mao, Chunhong Abraham, David Wattam, Alice R. Wilson, Meredith J.C. Shukla, Maulik Yoo, Hyun Seung Sobral, Bruno W. Curation, integration and visualization of bacterial virulence factors in PATRIC |
title | Curation, integration and visualization of bacterial virulence factors in PATRIC |
title_full | Curation, integration and visualization of bacterial virulence factors in PATRIC |
title_fullStr | Curation, integration and visualization of bacterial virulence factors in PATRIC |
title_full_unstemmed | Curation, integration and visualization of bacterial virulence factors in PATRIC |
title_short | Curation, integration and visualization of bacterial virulence factors in PATRIC |
title_sort | curation, integration and visualization of bacterial virulence factors in patric |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287947/ https://www.ncbi.nlm.nih.gov/pubmed/25273106 http://dx.doi.org/10.1093/bioinformatics/btu631 |
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