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135 | # include <semsim/SemSim.h>
# include "sbml/SBMLTypes.h"
# include <iostream>
using namespace semsim;
int main() {
// create SBML model
LIBSBML_CPP_NAMESPACE_QUALIFIER SBMLDocument* d =
new LIBSBML_CPP_NAMESPACE_QUALIFIER SBMLDocument(3, 2);
LIBSBML_CPP_NAMESPACE_QUALIFIER Model* m = d->createModel();
m->setId("beta_cell_model");
// create a compartment to represent the cytosol
LIBSBML_CPP_NAMESPACE_QUALIFIER Compartment* comp = m->createCompartment();
comp->setId("cytosol");
comp->setMetaId("cytosol");
comp->setSize(1);
comp->setConstant(true);
// add a CV term for the cytosol
LIBSBML_CPP_NAMESPACE_QUALIFIER CVTerm *cv_cytosol = new LIBSBML_CPP_NAMESPACE_QUALIFIER CVTerm();
cv_cytosol->setQualifierType(LIBSBML_CPP_NAMESPACE_QUALIFIER BIOLOGICAL_QUALIFIER);
cv_cytosol->setBiologicalQualifierType(LIBSBML_CPP_NAMESPACE_QUALIFIER BQB_IS);
cv_cytosol->addResource(GO::get(5829).getURI().encode());
comp->addCVTerm(cv_cytosol);
LIBSBML_CPP_NAMESPACE_QUALIFIER UnitDefinition* unitdef = m->createUnitDefinition();
unitdef->setId("molar");
LIBSBML_CPP_NAMESPACE_QUALIFIER Unit* unit = unitdef->createUnit();
unit->setKind(LIBSBML_CPP_NAMESPACE_QUALIFIER UNIT_KIND_MOLE);
unit->setExponent(1);
unit->setMultiplier(1);
unit->setScale(1);
unit = unitdef->createUnit();
unit->setKind(LIBSBML_CPP_NAMESPACE_QUALIFIER UNIT_KIND_LITRE);
unit->setExponent(-1);
unit->setMultiplier(1);
unit->setScale(1);
// create the species for glucose
LIBSBML_CPP_NAMESPACE_QUALIFIER Species* s = m->createSpecies();
s->setCompartment("cytosol");
s->setId("glucose");
s->setMetaId("glucose");
s->setInitialConcentration(0);
s->setUnits("molar");
s->setHasOnlySubstanceUnits(false);
s->setConstant(false);
s->setBoundaryCondition(false);
// add a CV term to glucose
LIBSBML_CPP_NAMESPACE_QUALIFIER CVTerm *cv_glucose = new LIBSBML_CPP_NAMESPACE_QUALIFIER CVTerm();
cv_glucose->setQualifierType(LIBSBML_CPP_NAMESPACE_QUALIFIER BIOLOGICAL_QUALIFIER);
cv_glucose->setBiologicalQualifierType(LIBSBML_CPP_NAMESPACE_QUALIFIER BQB_IS);
cv_glucose->addResource(CHEBI::get(17234).getURI().encode());
s->addCVTerm(cv_glucose);
// create import reaction for glucose
LIBSBML_CPP_NAMESPACE_QUALIFIER Reaction* reaction = m->createReaction();
reaction->setId("glucose_import");
reaction->setReversible(false);
LIBSBML_CPP_NAMESPACE_QUALIFIER SpeciesReference* sr = reaction->createProduct();
sr->setSpecies("glucose");
sr->setConstant(false);
LIBSBML_CPP_NAMESPACE_QUALIFIER KineticLaw* k = reaction->createKineticLaw();
LIBSBML_CPP_NAMESPACE_QUALIFIER Parameter* p = k->createParameter();
p->setId("glucose_import_rate");
p->setValue(1);
k->setMath(LIBSBML_CPP_NAMESPACE_QUALIFIER SBML_parseL3FormulaWithModel("glucose_import_rate", m));
// alternate way to set formula
// LIBSBML_CPP_NAMESPACE_QUALIFIER ASTNode* a =
// new LIBSBML_CPP_NAMESPACE_QUALIFIER ASTNode(LIBSBML_CPP_NAMESPACE_QUALIFIER AST_NAME);
// a->setName("glucose_import_rate");
// k->setMath(a);
LIBSBML_CPP_NAMESPACE_QUALIFIER SBMLWriter sbml_writer;
std::cerr << "**********************************************************\n";
std::cerr << "SBML output:\n";
std::cerr << "**********************************************************\n\n";
std::cerr << sbml_writer.writeSBMLToString(d) << "\n";
// importing the model into libSemSim will automatically
// add metaids for any annotatable SBML elements that lack them
SBMLImporter importer(d);
SBMLModel& model = importer.getSBMLModel();
std::cerr << "**********************************************************\n";
std::cerr << "RDF serialization of annotations:\n";
std::cerr << "**********************************************************\n\n";
std::cerr << model.getRDF("./mymodel.xml", "turtle") << "\n";
// this isn't bad - the RDF already contains a composite annotation
// telling is that the species "glucose" is inside the "cytosol"
// we currently have "cytosolic glucose"
// however - what we want is "cytosolic glucose in a pancreatic beta cell"
// to describe this, we need to annotate the compartment (not the species!)
// and describe the cell type it is part of
// the compartment currently has a *singular annotation*, which can't
// represent membership in a "pancreatic beta cell", so we change this to
// a composite annotation
Component* c = model.getComponentForId("cytosol");
c->setAnnotation(c->getAnnotation().makeComposite(OPB::get(523))); // 523 is spatial volume
// now add a descriptor term specifying that the cytoplasm
// is part of a pancreatic beta cell (CL:0000169)
c->getCompositeAnnotation().addTerm(
bqb::isPartOf, // the relation (the cytoplasm *is part of* ...)
CL::get(169) // the resource (pancreatic beta cell)
);
std::cerr << "**********************************************************\n";
std::cerr << "RDF serialization with cell type annotation:\n";
std::cerr << "**********************************************************\n\n";
std::cerr << model.getRDF("./mymodel.xml", "turtle") << "\n";
std::cerr << "**********************************************************\n";
std::cerr << "Humanized version of the annotation information\n";
std::cerr << "(ontology terms replaced by human-readable names):\n";
std::cerr << "**********************************************************\n\n";
std::cerr << model.humanize() << "\n";
return 0;
}
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