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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...

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Autores principales: Mao, Chunhong, Abraham, David, Wattam, Alice R., Wilson, Meredith J.C., Shukla, Maulik, Yoo, Hyun Seung, Sobral, Bruno W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
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.
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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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