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

TitleA community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Publication TypeJournal Article
Year of Publication2011
AuthorsThiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA, De Keersmaecker SCJ, Liao Y-C, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin S-il, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D
JournalBMC Syst Biol
Volume5
Pagination8
PubMed Date2011-1-20
ISSN1752-0509
KeywordsAnti-Bacterial Agents, Cooperative Behavior, Databases, Factual, Genes, Bacterial, Humans, Metabolic Networks and Pathways, Models, Biological, Salmonella typhimurium, Systems Biology
Abstract

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.

Alternate JournalBMC Syst Biol
PubMed ID21244678

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