A 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 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.


CONCLUSIONS
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.
Center for Systems Biology, University of Iceland, Reykjavik, Iceland.
Ines
I
Thiele
Daniel R
DR
Hyduke
Benjamin
B
Steeb
Guy
G
Fankam
Douglas K
DK
Allen
Susanna
S
Bazzani
Pep
P
Charusanti
Feng-Chi
FC
Chen
Ronan M T
RM
Fleming
Chao A
CA
Hsiung
Sigrid C J
SC
De Keersmaecker
Yu-Chieh
YC
Liao
Kathleen
K
Marchal
Monica L
ML
Mo
Emre
E
Özdemir
Anu
A
Raghunathan
Jennifer L
JL
Reed
Sook-il
SI
Shin
Sara
S
Sigurbjörnsdóttir
Jonas
J
Steinmann
Suresh
S
Sudarsan
Neil
N
Swainston
Inge M
IM
Thijs
Karsten
K
Zengler
Bernhard O
BO
Palsson
Joshua N
JN
Adkins
Dirk
D
Bumann
D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology; D003299:Cooperative Behavior; D016208:Databases, Factual; D005798:Genes, Bacterial / Q000235:genetics; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012486:Salmonella typhimurium / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D049490:Systems Biology
D000900:Anti-Bacterial Agents
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