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Nucleic Acids Research Advance Access first published online on November 16, 2006
This version published online on December 6, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl858
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PATRIC: The VBI PathoSystems Resource Integration Center

E. E. Snyder1,*, N. Kampanya1, J. Lu1, E. K. Nordberg1, H. R. Karur1, M. Shukla1, J. Soneja1, Y. Tian1, T. Xue1, H. Yoo1, F. Zhang1, C. Dharmanolla1, N. V. Dongre1, J. J. Gillespie1,4, J. Hamelius1, M. Hance1, K. I. Huntington1, D. Jukneliene2, J. Koziski1, L. Mackasmiel1, S. P. Mane1, V. Nguyen1, A. Purkayastha1, J. Shallom1, G. Yu1, Y. Guo1, J. Gabbard1,3, D. Hix1,3, A. F. Azad4, S. C. Baker2, S. M. Boyle5, Y. Khudyakov6, X. J. Meng5, C. Rupprecht6, J. Vinje6, O. R. Crasta1, M. J. Czar1, A. Dickerman1, J. D. Eckart1, R. Kenyon1, R. Will1, J. C. Setubal1 and B. W. S. Sobral1

1 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA 2 Department of Microbiology and Immunology, Loyola University Medical Center Maywood, IL 60153, USA 3 Center for Human–Computer Interaction, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA 4 Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD 21201, USA 5 VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA 6 Centers for Disease Control and Prevention, Atlanta GA 30333, USA

*To whom correspondence should be addressed. Tel: +1 540 231 5428; Fax: +1 540 231 2606; Email: eesnyder{at}vbi.vt.edu

Received August 15, 2006. Revised September 14, 2006. Accepted October 1, 2006.

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: ‘breadth first’ beginning with whole-genome and proteome curation using standardized protocols, a ‘targeted’ approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.

Present addresses:

Y. Guo, NIAID Office of Technology Information Systems (OTIS), Contractor, MSD Inc., Bethesda, MD 20892, USA

J. D. Eckart, Advanced Technology Division, Aflac, Columbus, GA 31999, USA


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