|Title||A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.|
|Publication Type||Journal Article|
|Year of Publication||2011|
|Authors||Thiele 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|
|Journal||BMC Syst Biol|
|Keywords||Anti-Bacterial Agents, Cooperative Behavior, Databases, Factual, Genes, Bacterial, Humans, Metabolic Networks and Pathways, Models, Biological, Salmonella typhimurium, Systems Biology|
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 Journal||BMC Syst Biol|