S.aureus_iSB619 {BiGGR} | R Documentation

## Metabolic reconstruction of S.aureus from the BiGG database

### Description

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(S.aureus_iSB619)

### 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

Becker, S.A. and Palsson, B.O., Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation, BMC Microbiology, 5(1):8 (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)
    S.aureus_iSB619 <- rsbml_read(text=string)

    ## End(Not run)

    ##load data and get all reaction IDs
    data(S.aureus_iSB619)
    model <- S.aureus_iSB619@model
    ##get all reaction identifiers
    sapply(model@reactions, id)

[Package BiGGR version 1.24.0 Index]