@article{17592baf72ec4c53b0a5e6893ecf4117,
title = "The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation",
abstract = "The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of ∼50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development.",
author = "McNeil, {Leslie Klis} and Claudia Reich and Aziz, {Ramy K.} and Daniela Bartels and Matthew Cohoon and Terry Disz and Edwards, {Robert A.} and Svetlana Gerdes and Kaitlyn Hwang and Michael Kubal and Margaryan, {Gohar Rem} and Folker Meyer and William Mihalo and Olsen, {Gary J.} and Robert Olson and Andrei Osterman and Daniel Paarmann and Tobias Paczian and Bruce Parrello and Pusch, {Gordon D.} and Rodionov, {Dmitry A.} and Xinghua Shi and Olga Vassieva and Veronika Vonstein and Olga Zagnitko and Fangfang Xia and Jenifer Zinner and Ross Overbeek and Rick Stevens",
note = "Funding Information: The National Microbial Pathogen Data Resource (NMPDR) is one of eight Bioinformatics Resource Centers funded by the National Institute of Allergy and Infectious Disease (NIAID) to provide the comprehensive bioinformatics environment needed to support research in biodefense, emerging infectious diseases, and re-emerging pathogens. The NMPDR focus organisms are NIAID Category B priority pathogens, including the food and water-borne diarrheagenic bacteria Campylobacter jejuni, Vibrio cholerae, Vibrio para-haemolyticus, Vibrio vulnificus, and Listeria monocytogenes. Also included are the nosocomial pathogens Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes (Group A Strep). NMPDR is both a central repository for a wide variety of scientific data on these pathogenic Funding Information: This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400042C. Funding to pay the Open Access publication charges for this article was provided by NIH Contract No. HHSN266200400042C.",
year = "2007",
month = jan,
doi = "10.1093/nar/gkl947",
language = "English (US)",
volume = "35",
pages = "D347--D353",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",
}