The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation

Leslie Klis McNeil; Claudia Reich; Ramy K. Aziz; Daniela Bartels; Matthew Cohoon; Terry Disz; Robert A. Edwards; Svetlana Gerdes; Kaitlyn Hwang; Michael Kubal; Gohar Rem Margaryan; Folker Meyer; William Mihalo; Gary J. Olsen; Robert Olson; Andrei Osterman; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D. Pusch; Dmitry A. Rodionov; Xinghua Shi; Olga Vassieva; Veronika Vonstein; Olga Zagnitko; Fangfang Xia; Jenifer Zinner; Ross Overbeek; Rick Stevens

doi:10.1093/nar/gkl947

The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation

Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. PuschDmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross Overbeek, Rick Stevens

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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.

Original language	English
Pages (from-to)	D347-D353
Journal	Nucleic Acids Research
Volume	35
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkl947
Publication status	Published - Jan 2007
Externally published	Yes

Bibliographical note

Oxford University Press (OUP) has partnered with Copyright Clearance Center's RightsLink service to offer a variety of options for reusing this content. Note: This article is available under the Creative Commons CC-BY-NC license and permits non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited. For commercial reuse, permission must be requested below.

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McNeil, L. K., Reich, C., Aziz, R. K., Bartels, D., Cohoon, M., Disz, T., Edwards, R. A., Gerdes, S., Hwang, K., Kubal, M., Margaryan, G. R., Meyer, F., Mihalo, W., Olsen, G. J., Olson, R., Osterman, A., Paarmann, D., Paczian, T., Parrello, B., ... Stevens, R. (2007). The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Research, 35(SUPPL. 1), D347-D353. https://doi.org/10.1093/nar/gkl947

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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 = "Oxford University Press (OUP) has partnered with Copyright Clearance Center's RightsLink service to offer a variety of options for reusing this content. Note: This article is available under the Creative Commons CC-BY-NC license and permits non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited. For commercial reuse, permission must be requested below.",

year = "2007",

month = jan,

doi = "10.1093/nar/gkl947",

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volume = "35",

pages = "D347--D353",

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McNeil, LK, Reich, C, Aziz, RK, Bartels, D, Cohoon, M, Disz, T, Edwards, RA, Gerdes, S, Hwang, K, Kubal, M, Margaryan, GR, Meyer, F, Mihalo, W, Olsen, GJ, Olson, R, Osterman, A, Paarmann, D, Paczian, T, Parrello, B, Pusch, GD, Rodionov, DA, Shi, X, Vassieva, O, Vonstein, V, Zagnitko, O, Xia, F, Zinner, J, Overbeek, R & Stevens, R 2007, 'The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation', Nucleic Acids Research, vol. 35, no. SUPPL. 1, pp. D347-D353. https://doi.org/10.1093/nar/gkl947

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T2 - A genomics platform based on subsystem annotation

AU - McNeil, Leslie Klis

AU - Reich, Claudia

AU - Aziz, Ramy K.

AU - Bartels, Daniela

AU - Cohoon, Matthew

AU - Disz, Terry

AU - Edwards, Robert A.

AU - Gerdes, Svetlana

AU - Hwang, Kaitlyn

AU - Kubal, Michael

AU - Margaryan, Gohar Rem

AU - Meyer, Folker

AU - Mihalo, William

AU - Olsen, Gary J.

AU - Olson, Robert

AU - Osterman, Andrei

AU - Paarmann, Daniel

AU - Paczian, Tobias

AU - Parrello, Bruce

AU - Pusch, Gordon D.

AU - Rodionov, Dmitry A.

AU - Shi, Xinghua

AU - Vassieva, Olga

AU - Vonstein, Veronika

AU - Zagnitko, Olga

AU - Xia, Fangfang

AU - Zinner, Jenifer

AU - Overbeek, Ross

AU - Stevens, Rick

N1 - Oxford University Press (OUP) has partnered with Copyright Clearance Center's RightsLink service to offer a variety of options for reusing this content. Note: This article is available under the Creative Commons CC-BY-NC license and permits non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited. For commercial reuse, permission must be requested below.

PY - 2007/1

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N2 - 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.

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AN - SCOPUS:33846119130

SN - 0305-1048

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ER -

The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation

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