E.coli_textbook: Ecoli dataset from the BiGG database

In hettling/BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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)

hettling/BiGGR documentation built on April 17, 2020, 5:19 a.m.