buildSBMLFromBiGG {BiGGR} | R Documentation

## Build an SBML model from a given reactions file obtained from the BiGG database

### Description

Creates an SBML model containing all species, reactions and compartments that occur in a reactions file obtained from the BiGG database.

### Usage

    buildSBMLFromBiGG(reactions.filename, model.id=character(0), model.name=character(0))

### Arguments

`reactions.filename` | name of the file containing the reactions extracted from BiGG
`model.id` | id for the SBML model created by the function. Defaults to `reactions.filename`
`model.name` | name for the SBML model created by the function. Defaults to `reactions.filename`

### Value

a rsbml `Model` object containing all reactions, species and compartments that are associated with the reactions in the given input file.

### Note

Note that it can be the case that species can be present in multiple compartments. In order to avoid any ambiguities in the model returned by the function, each species identifier is composed of the species identifier given in the reactions file and the compartment identifier, joined by "_". Example: adp in compartment c (cytosol) has the id `adp_c`.

### Author(s)

Anand Gavai, Hannes Hettling

### References

Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. , BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BMC Bioinformatics, 11:213, (2010). http://bigg.ucsd.edu/

### See Also

`createLIMFromSBML`

### Examples

    ##build model from file Reactions.txt from the package examples
    path <- system.file("extdata", "Reactions.txt", package="BiGGR")
    model <- buildSBMLFromBiGG(path, model.id="myid")

[Package BiGGR version 1.20.0 Index]