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PMID: 17142235 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

PATRIC: the VBI PathoSystems Resource Integration Center.

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D401-6

Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW

Abstract

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.

MeSH Terms
Bioterrorism Databases, Genetic Genomics Internet Proteobacteria/genetics,metabolism,pathogenicity Proteomics RNA Viruses/genetics,metabolism,pathogenicity Systems Integration User-Computer Interface
Authors & Affiliations
43 authors, click to expand affiliations / ORCID
Snyder E E
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. eesnyder@vbi.vt.edu
Kampanya N
Lu J
Nordberg E K
Karur H R
Shukla M
Soneja J
Tian Y
Xue T
Yoo H
Zhang F
Dharmanolla C
Dongre N V
Gillespie J J
Hamelius J
Hance M
Huntington K I
Jukneliene D
Koziski J
Mackasmiel L
Mane S P
Nguyen V
Purkayastha A
Shallom J
Yu G
Guo Y
Gabbard J
Hix D
Azad A F
Baker S C
Boyle S M
Khudyakov Y
Meng X J
Rupprecht C
Vinje J
Crasta O R
Czar M J
Dickerman A
Eckart J D
Kenyon R
Will R
Setubal J C
Sobral B W S
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl858
Email
eesnyder@vbi.vt.edu
Published
2007-01-00
Epub
2006-00-16
Pages
D401-6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1669763
Subset
IM
Grants
PHS HHS · HHSN266200400035C · United States
External Links
PubMed source DOI: 10.1093/nar/gkl858 PMC Full Text View journal details
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