H.pylori_ilT341 {BiGGR} | R Documentation

## 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

### 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).

### Source

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

### 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)

[Package BiGGR version 1.20.0 Index]