loadSBML: Load an SBML document

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Load an SBML document

Description

Loads an SBML document that specifies a qualitative model using the sbml-qual extension package.

Usage

loadSBML(file, symbolic=FALSE)

Arguments

file	The SBML document to be imported
symbolic	If set to TRUE, the function returns an object of class SymbolicBooleanNetwork with an expression tree representation. Otherwise, it returns an object of class BooleanNetwork with a truth table representation.

Details

The import assumes an SBML level 3 version 1 document with the sbml-qual extension package version 1.0. BoolNet only supports a subset of the sbml-qual standard. The function tries to import those documents that describe a logical model with two possible values per species. It does not support general logical models with more than two values per species or Petri nets.

Further details on the import:

• The import supports multiple function terms with the same output for a transition and interprets them as a disjunction, as proposed in the specification.

• Comparison operators are converted to the corresponding Boolean expressions.

• Compartments are ignored.

For the import, the XML package is required.

Value

Returns a structure of class BooleanNetwork or SymbolicBooleanNetwork, as described in loadNetwork.

References

http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Qualitative_Models_(qual)

See Also

toSBML, loadNetwork

Examples

## Not run: 
# load the cell cycle network
data(cellcycle)

fil <- tempfile()
# export the network to SBML
toSBML(cellcycle, fil)

# reimport the model
print(loadSBML(fil))

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.