BiGGR (version 1.8.0)

E.coli_textbook: 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

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

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)