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 approximately 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.
authors.affiliation: National Center for Supercomputing Applications, Urbana, IL 61801, USA. lkmcneil@ncsa.uiuc.edu
authors.forename: Leslie Klis
authors.initials: LK
authors.lastname: McNeil
authors.forename: Claudia
authors.initials: C
authors.lastname: Reich
authors.forename: Ramy K
authors.initials: RK
authors.lastname: Aziz
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Matthew
authors.initials: M
authors.lastname: Cohoon
authors.forename: Terry
authors.initials: T
authors.lastname: Disz
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.forename: Kaitlyn
authors.initials: K
authors.lastname: Hwang
authors.forename: Michael
authors.initials: M
authors.lastname: Kubal
authors.forename: Gohar Rem
authors.initials: GR
authors.lastname: Margaryan
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: William
authors.initials: W
authors.lastname: Mihalo
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.forename: Andrei
authors.initials: A
authors.lastname: Osterman
authors.forename: Daniel
authors.initials: D
authors.lastname: Paarmann
authors.forename: Tobias
authors.initials: T
authors.lastname: Paczian
authors.forename: Bruce
authors.initials: B
authors.lastname: Parrello
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Xinghua
authors.initials: X
authors.lastname: Shi
authors.forename: Olga
authors.initials: O
authors.lastname: Vassieva
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
authors.forename: Olga
authors.initials: O
authors.lastname: Zagnitko
authors.forename: Fangfang
authors.initials: F
authors.lastname: Xia
authors.forename: Jenifer
authors.initials: J
authors.lastname: Zinner
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
mesh_terms: D001419:Bacteria / Q000187:drug effects / Q000378:metabolism / Q000472:pathogenicity; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology; D004269:DNA, Bacterial / Q000737:chemistry; D030561:Databases, Nucleic Acid; D016503:Drug Delivery Systems; D005798:Genes, Bacterial; D020043:Genes, Essential; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial