loadSBML function

Load an SBML document

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

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.

Returns

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)