BiGGR (version 1.8.0)

H.pylori_ilT341: H.pylori in silico genome-scale characterization of single and double deletion mutants

Description

An Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants. The dataset was generated by downloading the SBML file of the reconstruction (http://bigg.ucsd.edu/bigg/exportSelect.pl) which was subsequently converted into an object of class SBML using the rsbml_read function from the rsbml package.

Usage

data(H.pylori_ilT341)

Format

An sbml object of class rsbml

Source

http://bigg.ucsd.edu/bigg/exportSelect.pl

Details

Note that the files in the BiGG database fail the unit consistancy check of the rsbml_read function. To avoid unit checking when creating SBML objects, the substance units in the reaction tags were parsed out from the database SBML files (see example below).

References

Thiele, I., Vo, T.D., Price, N.D. and Palsson, B., An Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants, Journal of Bacteriology, 187(16): 5818-5830 (2005)

Examples

## Not run: 
# ##The dataset was generated as follows:
# ##SBML_export.xml was downloaded from http://bigg.ucsd.edu/bigg/exportSelect.pl
# ##and a newline was added at the end of the file
# file <- "SBML_export.xml"
# string <- paste(readLines(file), collapse="\n")
# ##Parse out units to avoid validation error
# string <- gsub("units=\".+?\"", "", string)
# H.pylori_ilT341 <- rsbml_read(text=string) 
# ## End(Not run)

##load data and get all reaction IDs
data(H.pylori_ilT341)
model <- H.pylori_ilT341@model
##get all reaction identifiers
sapply(model@reactions, id)