H.sapiens_Recon_1 {BiGGR} | R Documentation

## 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)

[Package BiGGR version 1.20.0 Index]