Composite Annotations: SBML Examples
Annotations on a Physical Entity
In this case we build a new model using tellurium and antimony in Python. For simplicity, the string was copied from Python and stored as a string for the C++ and C examples.
In the example we create a PhysicalEntity type annotation of A, which has the metid SpeciesA. Our annotation states that we are simulating the chemical concetration (OPB:OPB_00340) of Smad3 (uniprot/P84022’) in the dermal fibroblasts `fma/FMA:63877 of the dermal papilla fma:FMA:70737 in the skin FMA_7163 of the surface or the arm FMA:24178.
Note
You can add an arbitrary number of anatomical locations, but the order you add them is meaningful. The first anatomical location you add will be at the smallest level of biological organization which increases when you add more locations.
Demonstrate the creation of a physical entity composite annotation in Python
from pyomexmeta import RDF, eUriType
sbml = """<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model metaid="SimpleRegulation" id="SimpleRegulation">
<listOfCompartments>
<compartment id="cell" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="A" metaid="SpeciesA" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="B" metaid="SpeciesB" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="C" metaid="SpeciesC" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="D" metaid="SpeciesD" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="S" metaid="S" value="0" constant="true"/>
<parameter id="k1" metaid="k1" value="0.1" constant="true"/>
<parameter id="k2" metaid="k2" value="0.1" constant="true"/>
<parameter id="k3" metaid="k3" value="0.1" constant="true"/>
<parameter id="k4" metaid="k4" value="0.1" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="R1" metaid="R1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> A </ci>
<ci> S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R2" metaid="R2" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R3" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="B"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3 </ci>
<ci> C </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R4" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4 </ci>
<ci> D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(sbml, generate_new_metaids=True, sbml_semantic_extraction=False)
sbml_with_metaids = editor.get_xml()
print(sbml_with_metaids)
with editor.new_physical_entity() as physical_entity:
physical_entity \
.about("SpeciesA", eUriType.MODEL_URI) \
.identity("uniprot/PD12345") \
.is_part_of("fma:1234") \
.has_property( "EntityProperty", eUriType.LOCAL_URI, "opb:OPB_12345")
print(rdf)
Output
[16:33:33 +01:00] warning : XML parser warning: Unsupported version '1.1'
<?xml version="1.1" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model metaid="SimpleRegulation" id="SimpleRegulation">
<listOfCompartments>
<compartment id="cell" spatialDimensions="3" size="1" constant="true" metaid="compartment0000"/>
</listOfCompartments>
<listOfSpecies>
<species id="A" metaid="SpeciesA" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="B" metaid="SpeciesB" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="C" metaid="SpeciesC" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="D" metaid="SpeciesD" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="S" metaid="S" value="0" constant="true"/>
<parameter id="k1" metaid="k1" value="0.1" constant="true"/>
<parameter id="k2" metaid="k2" value="0.1" constant="true"/>
<parameter id="k3" metaid="k3" value="0.1" constant="true"/>
<parameter id="k4" metaid="k4" value="0.1" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="R1" metaid="R1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> A </ci>
<ci> S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R2" metaid="R2" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R3" reversible="false" fast="false" metaid="reaction0000">
<listOfReactants>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="B"/>
</listOfModifiers>
<kineticLaw metaid="kineticLaw0000">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3 </ci>
<ci> C </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R4" reversible="false" fast="false" metaid="reaction0001">
<listOfReactants>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="kineticLaw0001">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4 </ci>
<ci> D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:EntityProperty
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_12345> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA>
bqbiol:is <https://identifiers.org/uniprot/PD12345> ;
bqbiol:isPartOf <https://identifiers.org/fma:1234> .
Demonstrate the creation of a physical entity composite annotation in C++
#include <iostream>
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main(){
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"SimpleRegulation\" id=\"SimpleRegulation\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cell\" spatialDimensions=\"3\" size=\"1\" constant=\"true\" metaid=\"omexMetaId0000\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"A\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesA\"/>\n"
" <species id=\"B\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesB\"/>\n"
" <species id=\"C\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesC\"/>\n"
" <species id=\"D\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesD\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"S\" metaid=\"S\" value=\"0\" constant=\"true\"/>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k3\" metaid=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" metaid=\"Reaction1\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction1\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k1 </ci>\n"
" <ci> A </ci>\n"
" <ci> S </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R2\" reversible=\"false\" fast=\"false\" metaid=\"Reaction2\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k2 </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R3\" reversible=\"false\" fast=\"false\" metaid=\"omexMetaId0009\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <listOfModifiers>\n"
" <modifierSpeciesReference species=\"B\"/>\n"
" </listOfModifiers>\n"
" <kineticLaw metaid=\"omexMetaId0010\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k3 </ci>\n"
" <ci> C </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R4\" reversible=\"false\" fast=\"false\" metaid=\"omexMetaId0011\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"omexMetaId0012\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k4 </ci>\n"
" <ci> D </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF rdf;
Editor editor = rdf.toEditor(sbml, true, true);
PhysicalEntity physicalEntity = editor.newPhysicalEntity();
physicalEntity
.about("SimpleRegulation", MODEL_URI)
.identity("uniprot/PD12345")
.isPartOf("fma:1234")
.hasProperty("opb:OPB_12345");
editor.addPhysicalEntity(physicalEntity);
std::cout << rdf.toString() << std::endl;
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:EntityProperty0000
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#SimpleRegulation> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_12345> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:ProcessProperty0000
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#Reaction1> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0001
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#Reaction2> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0002
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#omexMetaId0009> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0003
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#omexMetaId0011> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SinkParticipant0001
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
local:SinkParticipant0002
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesD> .
local:SinkParticipant0003
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
local:SourceParticipant0001
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SourceParticipant0002
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:SourceParticipant0003
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesD> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#Reaction1>
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#Reaction2>
semsim:hasSinkParticipant local:SinkParticipant0001 ;
semsim:hasSourceParticipant local:SourceParticipant0001 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#SimpleRegulation>
bqbiol:is <https://identifiers.org/uniprot/PD12345> ;
bqbiol:isPartOf <https://identifiers.org/fma:1234> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#omexMetaId0009>
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0002 ;
semsim:hasSourceParticipant local:SourceParticipant0002 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#omexMetaId0011>
semsim:hasSinkParticipant local:SinkParticipant0003 ;
semsim:hasSourceParticipant local:SourceParticipant0003 .
Demonstrate the creation of a physical entity composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main(){
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"SimpleRegulation\" id=\"SimpleRegulation\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cell\" spatialDimensions=\"3\" size=\"1\" constant=\"true\" metaid=\"OmexMetaId0000\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"A\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesA\"/>\n"
" <species id=\"B\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesB\"/>\n"
" <species id=\"C\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesC\"/>\n"
" <species id=\"D\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesD\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"S\" metaid=\"S\" value=\"0\" constant=\"true\"/>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k3\" metaid=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" metaid=\"Reaction1\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction1\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k1 </ci>\n"
" <ci> A </ci>\n"
" <ci> S </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R2\" reversible=\"false\" fast=\"false\" metaid=\"Reaction2\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k2 </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R3\" reversible=\"false\" fast=\"false\" metaid=\"#OmexMetaId0009\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <listOfModifiers>\n"
" <modifierSpeciesReference species=\"B\"/>\n"
" </listOfModifiers>\n"
" <kineticLaw metaid=\"#OmexMetaId0010\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k3 </ci>\n"
" <ci> C </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R4\" reversible=\"false\" fast=\"false\" metaid=\"#OmexMetaId0011\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"#OmexMetaId0012\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k4 </ci>\n"
" <ci> D </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF* rdf = RDF_new();
Editor* editor = RDF_toEditor(rdf, sbml, true, false);
PhysicalEntity* physicalEntity = Editor_newPhysicalEntity(editor);
PhysicalEntity_about(physicalEntity,"SpeciesA", MODEL_URI);
PhysicalEntity_identity(physicalEntity, "uniprot/PD12345");
PhysicalEntity_isPartOf(physicalEntity, "fma:1234", IDENTIFIERS_URI);
// the full signature of has property (no function overloading in C)
PhysicalEntity_hasPropertyFull(physicalEntity, "EntityProperty", LOCAL_URI, "opb:OPB_12345");
Editor_addPhysicalEntity(editor, physicalEntity);
char* rdf_string = RDF_toString(rdf, "turtle");
printf("%s\n", rdf_string);
free(rdf_string);
PhysicalEntity_delete(physicalEntity);
Editor_delete(editor);
RDF_delete(rdf);
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:EntityProperty
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_12345> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA>
bqbiol:is <https://identifiers.org/uniprot/PD12345> ;
bqbiol:isPartOf <https://identifiers.org/fma:1234> .
Annotations on a Physical Process
Demonstrate the creation of a physical process composite annotation in Python
from pyomexmeta import RDF, eUriType
sbml = """<?xml version="1.1" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model metaid="SimpleRegulation" id="SimpleRegulation">
<listOfCompartments>
<compartment id="cell" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="A" metaid="A" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="B" metaid="B" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="C" metaid="C" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="D" metaid="D" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="S" metaid="S" value="0" constant="true"/>
<parameter id="k1" metaid="k1" value="0.1" constant="true"/>
<parameter id="k2" metaid="k2" value="0.1" constant="true"/>
<parameter id="k3" metaid="k3" value="0.1" constant="true"/>
<parameter id="k4" metaid="k4" value="0.1" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="R1" metaid="R1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> A </ci>
<ci> S </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R2" metaid="R2" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="B" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="A" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R3" metaid="R3" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="B"/>
</listOfModifiers>
<kineticLaw metaid="KineticLawForReaction3">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3 </ci>
<ci> C </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R4" metaid="R4" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="D" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="C" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw metaid="KineticLawForReaction4">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k4 </ci>
<ci> D </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(sbml, generate_new_metaids=False, sbml_semantic_extraction=False)
# For when generate_new_metaids=True
# sbml_with_metaids = editor.get_xml()
# print(sbml_with_metaids)
# annotate reaction R1as the chemical concentration
# flow rate OPB:OPB_00593 of Smad3 to phosphorylated smad3
with editor.new_physical_process() as physical_process:
physical_process \
.about("R1", eUriType.MODEL_URI) \
.is_version_of("GO/GO12345") \
.add_source(physical_entity_reference="SpeciesA", uri_type=eUriType.MODEL_URI, multiplier=1) \
.add_sink(physical_entity_reference="SpeciesB", uri_type=eUriType.MODEL_URI, multiplier=1) \
.add_mediator(physical_entity_reference="SpeciesC", uri_type=eUriType.MODEL_URI) \
.has_property(is_version_of="OPB:OPB_00593")
print(rdf)
Output
[16:33:33 +01:00] warning : XML parser warning: Unsupported version '1.1'
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:ProcessProperty0000
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R1> ;
bqbiol:isVersionOf <https://identifiers.org/OPB:OPB_00593> .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R1>
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 ;
bqbiol:isVersionOf <https://identifiers.org/GO/GO12345> .
Demonstrate the creation of a physical process composite annotation in C++
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main(){
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"SimpleRegulation\" id=\"SimpleRegulation\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cell\" spatialDimensions=\"3\" size=\"1\" constant=\"true\" metaid=\"OmexMetaId0000\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"A\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesA\"/>\n"
" <species id=\"B\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesB\"/>\n"
" <species id=\"C\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesC\"/>\n"
" <species id=\"D\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesD\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"S\" metaid=\"S\" value=\"0\" constant=\"true\"/>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k3\" metaid=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" metaid=\"R1\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction1\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k1 </ci>\n"
" <ci> A </ci>\n"
" <ci> S </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R2\" reversible=\"false\" fast=\"false\" metaid=\"R2\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k2 </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R3\" reversible=\"false\" fast=\"false\" metaid=\"R3\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <listOfModifiers>\n"
" <modifierSpeciesReference species=\"B\"/>\n"
" </listOfModifiers>\n"
" <kineticLaw metaid=\"KineticLawForReaction3\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k3 </ci>\n"
" <ci> C </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R4\" reversible=\"false\" fast=\"false\" metaid=\"R4\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction4\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k4 </ci>\n"
" <ci> D </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF rdf = RDF();
Editor editor = rdf.toEditor(sbml, true);
PhysicalProcess physicalProcess = editor.newPhysicalProcess();
physicalProcess.about("R1", MODEL_URI)
.addSource("SpeciesA", MODEL_URI, 1)
.addSink("SpeciesB", MODEL_URI, 1)
.addMediator("SpeciesC", MODEL_URI )
.hasProperty("opb:OPB_00592")
.isVersionOf("GO:12345");
editor.addPhysicalProcess(physicalProcess);
std::cout << rdf.toString() << std::endl; // turtle default
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:MediatorParticipant0001
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:ProcessProperty0000
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R1> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0001
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R2> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0002
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R3> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0003
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R4> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:ProcessProperty0004
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R1> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SinkParticipant0001
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
local:SinkParticipant0002
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesD> .
local:SinkParticipant0003
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:SinkParticipant0004
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
local:SourceParticipant0001
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SourceParticipant0002
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:SourceParticipant0003
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesD> .
local:SourceParticipant0004
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R1>
semsim:hasMediatorParticipant local:MediatorParticipant0001 ;
semsim:hasSinkParticipant local:SinkParticipant0000, local:SinkParticipant0004 ;
semsim:hasSourceParticipant local:SourceParticipant0000, local:SourceParticipant0004 ;
bqbiol:isVersionOf <https://identifiers.org/GO:12345> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R2>
semsim:hasSinkParticipant local:SinkParticipant0001 ;
semsim:hasSourceParticipant local:SourceParticipant0001 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R3>
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0002 ;
semsim:hasSourceParticipant local:SourceParticipant0002 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R4>
semsim:hasSinkParticipant local:SinkParticipant0003 ;
semsim:hasSourceParticipant local:SourceParticipant0003 .
Demonstrate the creation of a physical process composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main(){
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"SimpleRegulation\" id=\"SimpleRegulation\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cell\" spatialDimensions=\"3\" size=\"1\" constant=\"true\" metaid=\"OmexMetaId0000\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"A\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesA\"/>\n"
" <species id=\"B\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesB\"/>\n"
" <species id=\"C\" compartment=\"cell\" initialConcentration=\"10\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesC\"/>\n"
" <species id=\"D\" compartment=\"cell\" initialConcentration=\"0\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" metaid=\"SpeciesD\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"S\" metaid=\"S\" value=\"0\" constant=\"true\"/>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k3\" metaid=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k4\" value=\"0.1\" constant=\"true\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" metaid=\"R1\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction1\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k1 </ci>\n"
" <ci> A </ci>\n"
" <ci> S </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R2\" reversible=\"false\" fast=\"false\" metaid=\"R2\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"B\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"A\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k2 </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R3\" reversible=\"false\" fast=\"false\" metaid=\"R3\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <listOfModifiers>\n"
" <modifierSpeciesReference species=\"B\"/>\n"
" </listOfModifiers>\n"
" <kineticLaw metaid=\"KineticLawForReaction3\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k3 </ci>\n"
" <ci> C </ci>\n"
" <ci> B </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"R4\" reversible=\"false\" fast=\"false\" metaid=\"R4\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"D\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"C\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw metaid=\"KineticLawForReaction4\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> k4 </ci>\n"
" <ci> D </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF* rdf_ptr = RDF_new();
//
Editor* editor_ptr = RDF_toEditor(rdf_ptr, sbml, true, false);
PhysicalProcess* process = Editor_newPhysicalProcess(editor_ptr);
PhysicalProcess_about(process, "R1", MODEL_URI);
PhysicalProcess_addSource(process, "SpeciesA", MODEL_URI, 1.0);
PhysicalProcess_addSink(process, "SpeciesB", MODEL_URI, 1.0);
PhysicalProcess_addMediator(process, "SpeciesC", MODEL_URI);
PhysicalProcess_hasPropertyisVersionOf(process, "opb:OPB_00592");
PhysicalProcess_isVersionOf(process, "GO:12345", eUriType::IDENTIFIERS_URI);
Editor_addPhysicalProcess(editor_ptr, process);
char* rdf_string = RDF_toString(rdf_ptr, "turtle");
printf("%s\n", rdf_string);
free(rdf_string);
PhysicalProcess_delete(process);
Editor_delete(editor_ptr);
RDF_delete(rdf_ptr);
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesC> .
local:ProcessProperty0000
bqbiol:isPropertyOf <http://omex-library.org/NewOmex.omex/NewModel.xml#R1> ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesB> .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#SpeciesA> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#R1>
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 ;
bqbiol:isVersionOf <https://identifiers.org/GO:12345> .
Annotations on an energy differential
Demonstrate the creation of a energy differential composite annotation in Python
from pyomexmeta import RDF, eUriType
sbml = """<?xml version=\"1.0\" encoding=\"UTF-8\"?>
<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">
<model metaid=\"EnergyDiff\" id=\"EnergyDiff\">
<listOfCompartments>
<compartment id=\"cytoplasm\" metaid=\"cytoplasm\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>
<compartment id=\"extracellular\" metaid=\"extracellular\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>
</listOfCompartments>
<listOfSpecies>
<species id=\"Ca_ex\" metaid=\"Ca_ex\" compartment=\"extracellular\" initialConcentration=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>
<species id=\"Ca_cyt\" metaid=\"Ca_cyt\" compartment=\"cytoplasm\" initialConcentration=\"0.3\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>
</listOfSpecies>
<listOfParameters>
<parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>
<parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>
<parameter id=\"N_Ca\" metaid=\"NernstPotential\"/>
</listOfParameters>
<listOfReactions>
<reaction id=\"NernstReversalPotential_in\" metaid=\"NernstReversalPotential_in\" reversible=\"false\" fast=\"false\">
<listOfReactants>
<speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>
</listOfReactants>
<listOfProducts>
<speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>
</listOfProducts>
<kineticLaw>
<math xmlns=\"http://www.w3.org/1998/Math/MathML\">
<apply>
<times/>
<ci> cytoplasm </ci>
<ci> k1 </ci>
<ci> Ca_ex </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id=\"NernstReversalPotential_out\" metaid=\"NernstReversalPotential_out\" reversible=\"false\" fast=\"false\">
<listOfReactants>
<speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>
</listOfReactants>
<listOfProducts>
<speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>
</listOfProducts>
<kineticLaw>
<math xmlns=\"http://www.w3.org/1998/Math/MathML\">
<apply>
<times/>
<ci> extracellular </ci>
<ci> k2 </ci>
<ci> Ca_cyt </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(sbml, generate_new_metaids=True, sbml_semantic_extraction=False)
# Property: Osmotic Pressure
with editor.new_energy_diff() as energy_diff:
# about(): this could be named anything provided it is unique to the rdf graph because it is a LOCAL_URI
energy_diff.about(about="MembranePotential", uri_type=eUriType.LOCAL_URI)
energy_diff.add_source(physical_entity_reference="Ca_ex", uri_type=eUriType.MODEL_URI)
energy_diff.add_sink(physical_entity_reference="Ca_cyt",uri_type= eUriType.MODEL_URI)
# for energy differentials we use the full signature of hasProperty.
# The arguments are as follows:
# - NernstPotential: the "about" value that is used for the property associated with the energy differential
# - MODEL_URI: the uri type for the previous argument. In SBML this is a <parameter> and therefore a MODEL_URI
# while in CellML this is a construct local to the rdf document (so LOCAL_URI)
# - OPB:OPB_01581: the OPB term associated with the property (isVersionOf)
energy_diff.has_property(property_about="NernstPotential", about_uri_type=eUriType.MODEL_URI, is_version_of="OPB:OPB_01581")
print(rdf)
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MembranePotential
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_cyt> .
local:SourceParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_ex> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#NernstPotential>
bqbiol:isPropertyOf local:MembranePotential ;
bqbiol:isVersionOf <https://identifiers.org/OPB:OPB_01581> .
Demonstrate the creation of a energy differential composite annotation in C++
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main() {
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"EnergyDiff\" id=\"EnergyDiff\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cytoplasm\" metaid=\"cytoplasm\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" <compartment id=\"extracellular\" metaid=\"extracellular\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"Ca_ex\" metaid=\"Ca_ex\" compartment=\"extracellular\" initialConcentration=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
" <species id=\"Ca_cyt\" metaid=\"Ca_cyt\" compartment=\"cytoplasm\" initialConcentration=\"0.3\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"N_Ca\" metaid=\"NernstPotential\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"NernstReversalPotential_in\" metaid=\"NernstReversalPotential_in\" reversible=\"false\" fast=\"false\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw>\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> cytoplasm </ci>\n"
" <ci> k1 </ci>\n"
" <ci> Ca_ex </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"NernstReversalPotential_out\" metaid=\"NernstReversalPotential_out\" reversible=\"false\" fast=\"false\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw>\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> extracellular </ci>\n"
" <ci> k2 </ci>\n"
" <ci> Ca_cyt </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF rdf;
Editor editor = rdf.toEditor(sbml, false, false);
EnergyDiff energyDiff = editor.newEnergyDiff();
energyDiff
// this could be named anything provided it is unique to the rdf graph because it is a LOCAL_URI
.about("MembranePotential", LOCAL_URI)
.addSource("Ca_ex", MODEL_URI)
.addSink("Ca_cyt", MODEL_URI)
// for energy differentials we use the full signature of hasProperty.
// The arguments are as follows:
// - NernstPotential: the "about" value that is used for the property associated with the energy differential
// - MODEL_URI: the uri type for the previous argument. In SBML this is a <parameter> and therefore a MODEL_URI
// while in CellML this is a construct local to the rdf document (so LOCAL_URI)
// - OPB:OPB_01581: the OPB term associated with the property (isVersionOf)
.hasProperty("NernstPotential", MODEL_URI, "OPB:OPB_01581");
editor.addEnergyDiff(energyDiff);
std::cout << rdf.toString() << std::endl;
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MembranePotential
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_cyt> .
local:SourceParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_ex> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#NernstPotential>
bqbiol:isPropertyOf local:MembranePotential ;
bqbiol:isVersionOf <https://identifiers.org/OPB:OPB_01581> .
Demonstrate the creation of a energy differential composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main() {
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model metaid=\"EnergyDiff\" id=\"EnergyDiff\">\n"
" <listOfCompartments>\n"
" <compartment id=\"cytoplasm\" metaid=\"cytoplasm\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" <compartment id=\"extracellular\" metaid=\"extracellular\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"Ca_ex\" metaid=\"Ca_ex\" compartment=\"extracellular\" initialConcentration=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
" <species id=\"Ca_cyt\" metaid=\"Ca_cyt\" compartment=\"cytoplasm\" initialConcentration=\"0.3\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
" </listOfSpecies>\n"
" <listOfParameters>\n"
" <parameter id=\"k1\" metaid=\"k1\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"k2\" metaid=\"k2\" value=\"0.1\" constant=\"true\"/>\n"
" <parameter id=\"N_Ca\" metaid=\"NernstPotential\"/>\n"
" </listOfParameters>\n"
" <listOfReactions>\n"
" <reaction id=\"NernstReversalPotential_in\" metaid=\"NernstReversalPotential_in\" reversible=\"false\" fast=\"false\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw>\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> cytoplasm </ci>\n"
" <ci> k1 </ci>\n"
" <ci> Ca_ex </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" <reaction id=\"NernstReversalPotential_out\" metaid=\"NernstReversalPotential_out\" reversible=\"false\" fast=\"false\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"Ca_cyt\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"Ca_ex\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfProducts>\n"
" <kineticLaw>\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <times/>\n"
" <ci> extracellular </ci>\n"
" <ci> k2 </ci>\n"
" <ci> Ca_cyt </ci>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
" </reaction>\n"
" </listOfReactions>\n"
" </model>\n"
"</sbml>";
RDF* rdf = RDF_new();
Editor* editor = RDF_toEditor(rdf, sbml, false, false);
EnergyDiff* energyDiff = Editor_newEnergyDiff(editor);
// this could be named anything provided it is unique to the rdf graph because it is a LOCAL_URI
EnergyDiff_about(energyDiff, "MembranePotential", LOCAL_URI);
EnergyDiff_addSource(energyDiff, "Ca_ex", MODEL_URI);
EnergyDiff_addSink(energyDiff,"Ca_cyt", MODEL_URI);
// for energy differentials we use the full signature of hasProperty.
// The arguments are as follows:
// - NernstPotential: the "about" value that is used for the property associated with the energy differential
// - MODEL_URI: the uri type for the previous argument. In SBML this is a <parameter> and therefore a MODEL_URI
// while in CellML this is a construct local to the rdf document (so LOCAL_URI)
// - OPB:OPB_01581: the OPB term associated with the property (isVersionOf)
EnergyDiff_hasPropertyFull(energyDiff, "NernstPotential", MODEL_URI, "OPB:OPB_01581");
Editor_addEnergyDiff(editor, energyDiff);
std::cout << rdf->toString() << std::endl;
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MembranePotential
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_cyt> .
local:SourceParticipant0000
semsim:hasPhysicalEntityReference <http://omex-library.org/NewOmex.omex/NewModel.xml#Ca_ex> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#NernstPotential>
bqbiol:isPropertyOf local:MembranePotential ;
bqbiol:isVersionOf <https://identifiers.org/OPB:OPB_01581> .
Composite Annotations: CellML Examples
Annotations on a Physical Entity
Demonstrate the creation of a physical entity composite annotation in Python
from pyomexmeta import RDF, eUriType
cellml = """<?xml version=\"1.0\" encoding=\"UTF-8\"?>
<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">
<component name=\"main\">
<variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />
<variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />
<variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />
</component>
</model>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(cellml, generate_new_metaids=True, sbml_semantic_extraction=False)
sbml_with_metaids = editor.get_xml()
print(sbml_with_metaids)
with editor.new_physical_entity() as physical_entity:
physical_entity \
.about("entity0", eUriType.LOCAL_URI) \
.identity("fma:9570") \
.is_part_of("fma:18228") \
.has_property("main.Volume", eUriType.MODEL_URI, "opb:OPB_00154")
print(rdf)
Output
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://bime.uw.edu/semsim/#" xmlns:dc="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="annotation_examples" cmeta:id="annExamples">
<component name="main" cmeta:id="component0000">
<variable cmeta:id="main.Volume" initial_value="100" name="Volume" units="dimensionless"/>
<variable cmeta:id="main.MembraneVoltage" initial_value="-80" name="MembraneVoltage" units="dimensionless"/>
<variable cmeta:id="main.ReactionRate" initial_value="1" name="ReactionRate" units="dimensionless"/>
<variable cmeta:id="main.entity1" initial_value="1" name="entity1" units="dimensionless"/>
<variable cmeta:id="main.entity2" initial_value="1" name="entity2" units="dimensionless"/>
<variable cmeta:id="main.entity3" initial_value="1" name="entity3" units="dimensionless"/>
</component>
</model>
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:entity0
bqbiol:is <https://identifiers.org/fma:9570> ;
bqbiol:isPartOf <https://identifiers.org/fma:18228> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.Volume>
bqbiol:isPropertyOf local:entity0 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00154> .
Demonstrate the creation of a physical entity composite annotation in C++
#include <iostream>
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main(){
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF rdf;
Editor editor = rdf.toEditor(sbml, true, true);
PhysicalEntity physicalEntity = editor.newPhysicalEntity();
physicalEntity
.about("entity0", LOCAL_URI)
.identity("fma:9670")
.isPartOf("fma:18228")
.hasProperty("main.Volume", MODEL_URI, "opb:OPB_00154");//, "entity0", LOCAL_URI);
editor.addPhysicalEntity(physicalEntity);
std::cout << rdf.toString() << std::endl;
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:entity0
bqbiol:is <https://identifiers.org/fma:9670> ;
bqbiol:isPartOf <https://identifiers.org/fma:18228> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.Volume>
bqbiol:isPropertyOf local:entity0 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00154> .
Demonstrate the creation of a physical entity composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main(){
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF* rdf = RDF_new();
Editor* editor_ptr = RDF_toEditor(rdf, sbml, true, false);
PhysicalEntity* entity = Editor_newPhysicalEntity(editor_ptr);
entity = PhysicalEntity_about(entity, "entity0", LOCAL_URI);
entity = PhysicalEntity_identity(entity, "fma:9670");
entity = PhysicalEntity_isPartOf(entity, "fma:18228", IDENTIFIERS_URI);
entity = PhysicalEntity_hasPropertyFull(entity, "main.Volume", MODEL_URI, "opb:OPB_00154");
Editor_addPhysicalEntity(editor_ptr, entity);
Editor_addPhysicalEntity(editor_ptr, entity);
char* rdf_string = RDF_toString(rdf, "turtle");
printf("%s\n", rdf_string);
free(rdf_string);
PhysicalEntity_delete(entity);
Editor_delete(editor_ptr);
RDF_delete(rdf);
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:entity0
bqbiol:is <https://identifiers.org/fma:9670> ;
bqbiol:isPartOf <https://identifiers.org/fma:18228> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.Volume>
bqbiol:isPropertyOf local:entity0 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00154> .
Annotations on a Physical Process
Demonstrate the creation of a physical process composite annotation in Python
from pyomexmeta import RDF, eUriType
cellml = """<?xml version=\"1.0\" encoding=\"UTF-8\"?>
<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">
<component name=\"main\">
<variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />
<variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />
<variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />
</component>
</model>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(cellml, generate_new_metaids=True, sbml_semantic_extraction=False)
sbml_with_metaids = editor.get_xml()
with editor.new_physical_process() as physical_process:
physical_process.about("Process", eUriType.LOCAL_URI) \
.add_source("entity1", eUriType.LOCAL_URI, 1) \
.add_sink("entity2", eUriType.LOCAL_URI, 1) \
.add_mediator("entity3", eUriType.LOCAL_URI) \
.has_property("main.ReactionRate", eUriType.MODEL_URI, "opb:OPB_00592")
print(rdf)
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference local:entity3 .
local:Process
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity2 .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity1 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.ReactionRate>
bqbiol:isPropertyOf local:Process ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
Demonstrate the creation of a physical process composite annotation in C++
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main(){
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF rdf = RDF();
Editor editor = rdf.toEditor(sbml, true);
PhysicalProcess physicalProcess = editor.newPhysicalProcess();
physicalProcess.about("Process", LOCAL_URI)
.addSource("entity1", LOCAL_URI, 1)
.addSink("entity2", LOCAL_URI, 1)
.addMediator("entity3", LOCAL_URI)
.hasProperty("main.ReactionRate", MODEL_URI, "opb:OPB_00592");
editor.addPhysicalProcess(physicalProcess);
editor.addPhysicalProcess(physicalProcess);
std::cout << rdf.toString() << std::endl; // turtle default
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference local:entity3 .
local:Process
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity2 .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity1 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.ReactionRate>
bqbiol:isPropertyOf local:Process ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
Demonstrate the creation of a physical process composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main(){
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF* rdf_ptr = RDF_new();
//
Editor* editor_ptr = RDF_toEditor(rdf_ptr, sbml, true, false);
PhysicalProcess* physical_process_ptr = Editor_newPhysicalProcess(editor_ptr);
PhysicalProcess_about(physical_process_ptr, "Process", LOCAL_URI);
PhysicalProcess_addSource(physical_process_ptr, "entity1", LOCAL_URI, 1);
PhysicalProcess_addSink(physical_process_ptr, "entity2", LOCAL_URI, 1);
PhysicalProcess_addMediator(physical_process_ptr, "entity3", LOCAL_URI);
PhysicalProcess_hasPropertyFull(physical_process_ptr, "main.ReactionRate",MODEL_URI, "opb:OPB_00592");
Editor_addPhysicalProcess(editor_ptr, physical_process_ptr);
Editor_addPhysicalProcess(editor_ptr, physical_process_ptr);
char* rdf_string = RDF_toString(rdf_ptr, "turtle");
printf("%s\n", rdf_string);
free(rdf_string);
PhysicalProcess_delete(physical_process_ptr);
Editor_delete(editor_ptr);
RDF_delete(rdf_ptr);
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:MediatorParticipant0000
semsim:hasPhysicalEntityReference local:entity3 .
local:Process
semsim:hasMediatorParticipant local:MediatorParticipant0000 ;
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:SinkParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity2 .
local:SourceParticipant0000
semsim:hasMultiplier "1"^^rdf:double ;
semsim:hasPhysicalEntityReference local:entity1 .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.ReactionRate>
bqbiol:isPropertyOf local:Process ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
Annotations on an energy differential
Demonstrate the creation of a energy differential composite annotation in Python
from pyomexmeta import RDF, eUriType
cellml = """<?xml version=\"1.0\" encoding=\"UTF-8\"?>
<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">
<component name=\"main\">
<variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />
<variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />
<variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />
<variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />
</component>
</model>
"""
# create an empty RDF object
rdf = RDF()
editor = rdf.to_editor(cellml, generate_new_metaids=True, sbml_semantic_extraction=False)
with editor.new_physical_entity() as physical_entity:
physical_entity.about("entity0", eUriType.LOCAL_URI) \
.identity("fma:9570") \
.is_part_of("fma:18228") \
.has_property("main.Volume", eUriType.MODEL_URI, "opb:OPB_00154")
print(rdf)
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:entity0
bqbiol:is <https://identifiers.org/fma:9570> ;
bqbiol:isPartOf <https://identifiers.org/fma:18228> .
<http://omex-library.org/NewOmex.omex/NewModel.xml#main.Volume>
bqbiol:isPropertyOf local:entity0 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00154> .
Demonstrate the creation of a energy differential composite annotation in C++
#include "omexmeta/OmexMeta.h"
using namespace omexmeta;
int main(){
std::string sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF rdf = RDF();
Editor editor = rdf.toEditor(sbml, true);
EnergyDiff energy_diff = editor.newEnergyDiff();
energy_diff
.addSource("entity1", LOCAL_URI)
.addSink("entity2", LOCAL_URI)
.hasProperty("opb:OPB_00592");
editor.addEnergyDiff(energy_diff);
std::cout << rdf.toString() << std::endl; // turtle default
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:EnergyDiff0000
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:EnergyDiffProperty0000
bqbiol:isPropertyOf local:EnergyDiff0000 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:SinkParticipant0000
semsim:hasPhysicalEntityReference local:entity2 .
local:SourceParticipant0000
semsim:hasPhysicalEntityReference local:entity1 .
Demonstrate the creation of a energy differential composite annotation in C
#include "omexmeta/OmexMetaCApi.h"
using namespace omexmeta;
int main(){
const char* sbml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<model xmlns=\"http://www.cellml.org/cellml/1.1#\" xmlns:cmeta=\"http://www.cellml.org/metadata/1.0#\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:bqs=\"http://www.cellml.org/bqs/1.0#\" xmlns:semsim=\"http://bime.uw.edu/semsim/#\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" name=\"annotation_examples\" cmeta:id=\"annExamples\">\n"
" <component name=\"main\">\n"
" <variable cmeta:id=\"main.Volume\" initial_value=\"100\" name=\"Volume\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.MembraneVoltage\" initial_value=\"-80\" name=\"MembraneVoltage\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.ReactionRate\" initial_value=\"1\" name=\"ReactionRate\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity1\" initial_value=\"1\" name=\"entity1\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity2\" initial_value=\"1\" name=\"entity2\" units=\"dimensionless\" />\n"
" <variable cmeta:id=\"main.entity3\" initial_value=\"1\" name=\"entity3\" units=\"dimensionless\" />\n"
" </component>\n"
"</model>";
RDF* rdf = RDF_new();
Editor* editor = RDF_toEditor(rdf, sbml, true, false);
EnergyDiff* energyDiff = Editor_newEnergyDiff(editor);
EnergyDiff_addSink(energyDiff, "entity1", LOCAL_URI);
EnergyDiff_addSource(energyDiff, "entity2", LOCAL_URI);
EnergyDiff_hasPropertyisVersionOf(energyDiff, "opb:OPB_00592");
Editor_addEnergyDiff(editor, energyDiff);
char* rdf_string = RDF_toString(rdf, "turtle");
printf("%s\n", rdf_string);
free(rdf_string);
EnergyDiff_delete(energyDiff);
Editor_delete(editor);
RDF_delete(rdf);
return 0;
}
Output
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix bqbiol: <http://biomodels.net/biology-qualifiers/> .
@prefix semsim: <http://bime.uw.edu/semsim/> .
@prefix OMEXlib: <http://omex-library.org/> .
@prefix local: <http://omex-library.org/NewOmex.omex/NewModel.rdf#> .
local:EnergyDiff0000
semsim:hasSinkParticipant local:SinkParticipant0000 ;
semsim:hasSourceParticipant local:SourceParticipant0000 .
local:EnergyDiffProperty0000
bqbiol:isPropertyOf local:EnergyDiff0000 ;
bqbiol:isVersionOf <https://identifiers.org/opb:OPB_00592> .
local:SinkParticipant0000
semsim:hasPhysicalEntityReference local:entity1 .
local:SourceParticipant0000
semsim:hasPhysicalEntityReference local:entity2 .