community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Background: Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar...

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Published in:BMC systems biology Vol. 5; no. 1; p. 8
Main Authors: Thiele, Ines, Hyduke, Daniel R, Steeb, Benjamin, Fankam, Guy, Allen, Douglas K, Bazzani, Susanna, Charusanti, Pep, Chen, Feng-Chi, Fleming, Ronan M.T, Hsiung, Chao A, Keersmaecker, Sigrid C.J. de, Liao, Yu-Chieh, Marchal, Kathleen, Mo, Monica L, Özdemir, Emre, Raghunathan, Anu
Format: Journal Article
Language:English
Published: London BioMed Central 18.01.2011
BioMed Central Ltd
Subjects:
60 APPLIED LIFE SCIENCES
Algorithms
animal pathogenic bacteria
annotation
Anti-Bacterial Agents - metabolism
Anti-Bacterial Agents - pharmacology
Antibiotic resistance
ANTIBIOTICS
biochemical, genetic and genomic knowledge bases
biochemistry
Bioinformatics
BIOLOGY
Biomedical and Life Sciences
Cellular and Medical Topics
Community development
Computational Biology/Bioinformatics
Cooperative Behavior
Databases, Factual
DESIGN
DISEASES
Drug resistance
Escherichia-coli
Experimental design
Genes, Bacterial - genetics
Genetic aspects
genomes
genomics
Humans
IMPLEMENTATION
KNOWLEDGE BASE
Life Sciences
MATHEMATICAL MODELS
Metabolic Networks and Pathways
metabolic reconstructions
metabolism
microbial genetics
microbial physiology
Models, Biological
networks
Pathogenic microorganisms
PATHOGENS
Physiological
protein
PUBLIC HEALTH
reconstruction
Research Article
SALMONELLA
Salmonella enterica
Salmonella enterica subsp. enterica serovar Typhimurium
SALMONELLA TYPHIMURIUM
Salmonella typhimurium - drug effects
Salmonella typhimurium - genetics
Salmonella typhimurium - metabolism
Simulation and Modeling
Systems Biology
TARGETS
THERAPY
THERMODYNAMICS
United States
Network Reconstruction
Phenotype Microarray
Flux Balance Analysis
Metabolic Reconstruction
Metabolic Network Reconstruction
ISSN:1752-0509, 1752-0509
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Summary:Background: Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem. Results: Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches. Conclusion: Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.
Bibliography:http://dx.doi.org/10.1186/1752-0509-5-8
http://hdl.handle.net/10113/48641
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SourceType-Scholarly Journals-1
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USDOE
AC05-76RL01830
PNNL-SA-77733
ISSN:1752-0509
1752-0509
DOI:10.1186/1752-0509-5-8