E.coli_textbook {BiGGR} | R Documentation

## Ecoli dataset from the BiGG database

### Description

A metabolic reconstruction for Escherichia from text books. 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(E.coli_textbook)

### 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

Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.O., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information, olecular Systems Biology, 3:121 (2007)

### 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)
    E.coli_textbook <- rsbml_read(text=string)

    ## End(Not run)

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

[Package BiGGR version 1.16.0 Index]