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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Vydané v:	BMC systems biology Ročník 5; číslo 1; s. 8
Hlavní autori:	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
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 18.01.2011 BioMed Central Ltd
Predmet:	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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Shrnutí:	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.
Bibliografia:	http://dx.doi.org/10.1186/1752-0509-5-8 http://hdl.handle.net/10113/48641 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 USDOE AC05-76RL01830 PNNL-SA-77733
ISSN:	1752-0509 1752-0509
DOI:	10.1186/1752-0509-5-8