Reconstruction of human metabolism 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(H.sapiens_Recon_1)

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

Duarte, N.D., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., Palsson, B. O., Global reconstruction of the human metabolic network based on genomic and bibliomic data, Proc. Nat Acad. Sci. 104(6):1777-82 (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)
H.sapiens_Recon_1 <- rsbml_read(text=string) 

## End(Not run)

##load data and get all reaction IDs
data(H.sapiens_Recon_1)
model <- H.sapiens_Recon_1@model
##get all reaction identifiers
sapply(model@reactions, id)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BiGGR)
Error in library(BiGGR) : there is no package called 'BiGGR'
Execution halted