Article (Scientific journals)
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin et al.
2011In BMC Systems Biology, 5, p. 8
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Keywords :
Anti-Bacterial Agents/metabolism/pharmacology; Cooperative Behavior; Databases, Factual; Genes, Bacterial/genetics; Humans; Metabolic Networks and Pathways; Models, Biological; Salmonella typhimurium/drug effects/genetics/metabolism; Systems Biology
Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Thiele, Ines 
Hyduke, Daniel R.
Steeb, Benjamin
Fankam, Guy
Allen, Douglas K.
Bazzani, Susanna
Charusanti, Pep
Chen, Feng-Chi
Fleming, Ronan MT 
Hsiung, Chao A.
De Keersmaecker, Sigrid C. J.
Liao, Yu-Chieh
Marchal, Kathleen
Mo, Monica L.
Ozdemir, Emre
Raghunathan, Anu
Reed, Jennifer L.
Shin, Sook-Il
Sigurbjornsdottir, Sara
Steinmann, Jonas
Sudarsan, Suresh
Swainston, Neil
Thijs, Inge M.
Zengler, Karsten
Palsson, Bernhard O.
Adkins, Joshua N.
Bumann, Dirk
More authors (17 more) Less
External co-authors :
yes
Language :
English
Title :
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Publication date :
2011
Journal title :
BMC Systems Biology
ISSN :
1752-0509
Publisher :
BioMed Central, United Kingdom
Volume :
5
Pages :
8
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 30 April 2014

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