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[Sbfc-svn] SF.net SVN: sbfc:[673] trunk
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From: <tra...@us...> - 2016-07-15 07:14:13
|
Revision: 673
http://sourceforge.net/p/sbfc/code/673
Author: tramy-nguyen
Date: 2016-07-15 07:14:10 +0000 (Fri, 15 Jul 2016)
Log Message:
-----------
- Tested gene entity through both conversion.
- added missing default properties when converting BioPAX2SBML.
Modified Paths:
--------------
trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java
trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXConverter.java
trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
trunk/test/org/sbfc/test/biopax2sbml/InteractionTests.java
trunk/test/org/sbfc/test/biopax2sbml/PhysicalEntityTests.java
trunk/test/org/sbfc/test/resources/biopax3-template-reaction.owl
Added Paths:
-----------
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-genetic-interaction.xml
trunk/test/org/sbfc/test/sbml2biopax/outputFiles/
trunk/test/org/sbfc/test/sbml2biopax/outputFiles/biopax3-genetic-interaction.owl
Modified: trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java
===================================================================
--- trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java 2016-07-15 07:14:10 UTC (rev 673)
@@ -970,7 +970,9 @@
private void parsePhysicalInteraction(Interaction entity, org.sbml.jsbml.Model sbmlModel) throws ConversionException
{
Reaction reaction = setReaction(entity, sbmlModel);
-
+ reaction.setReversible(false);
+ reaction.setFast(false);
+
if (entity instanceof TemplateReaction)
{
parseTemplateReaction((TemplateReaction) entity, reaction);
@@ -1170,6 +1172,7 @@
private void parseConversionInteraction(Conversion conversion, org.sbml.jsbml.Model sbmlModel) throws ConversionException
{
Reaction reaction = setReaction(conversion, sbmlModel);
+ reaction.setFast(false);
if( conversion.getConversionDirection() != null && (conversion.getConversionDirection().equals(ConversionDirectionType.LEFT_TO_RIGHT) ||
conversion.getConversionDirection().equals(ConversionDirectionType.REVERSIBLE)))
Modified: trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXConverter.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXConverter.java 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXConverter.java 2016-07-15 07:14:10 UTC (rev 673)
@@ -189,13 +189,13 @@
if(interaction instanceof GeneticInteraction)
{
Species species = sbmlModel.getSpecies(modifier.getSpecies());
- Gene gene = sbml2BioPAXUtilities.createGeneFromSpecies(bpModel, species);
+ Gene gene = sbml2BioPAXUtilities.convertGeneFromSpecies(bpModel, species);
interaction.addParticipant(gene);
}
else if(interaction instanceof TemplateReaction)
{
Species species = sbmlModel.getSpecies(modifier.getSpecies());
- PhysicalEntity physicalEntity = sbml2BioPAXUtilities.convertSpecies(bpModel, species);
+ PhysicalEntity physicalEntity = (PhysicalEntity) sbml2BioPAXUtilities.convertSpecies(bpModel, species);
if(physicalEntity instanceof Dna || physicalEntity instanceof Rna || physicalEntity instanceof Protein)
{
interaction.addParticipant(physicalEntity);
@@ -206,7 +206,7 @@
pathway.addPathwayComponent(control);
control.addControlled(interaction);
Species species = sbmlModel.getSpecies(modifier.getSpecies());
- Controller controller = sbml2BioPAXUtilities.convertSpecies(bpModel, species);
+ Controller controller = (Controller) sbml2BioPAXUtilities.convertSpecies(bpModel, species);
control.addController(controller);
}
// Modifiers -> Controls [end]
@@ -220,7 +220,7 @@
for (SpeciesReference speciesRef : listOfSpeciesReferences) {
Species species = sbmlModel.getSpecies(speciesRef.getSpecies());
- PhysicalEntity physicalEntity = sbml2BioPAXUtilities.convertSpecies(bpModel, species);
+ PhysicalEntity physicalEntity = (PhysicalEntity) sbml2BioPAXUtilities.convertSpecies(bpModel, species);
if(interaction instanceof Conversion){
Conversion conversion = (Conversion) interaction;
if(isProduct)
Modified: trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2016-07-15 07:14:10 UTC (rev 673)
@@ -29,6 +29,7 @@
import org.biopax.paxtools.model.level3.DnaReference;
import org.biopax.paxtools.model.level3.DnaRegion;
import org.biopax.paxtools.model.level3.DnaRegionReference;
+import org.biopax.paxtools.model.level3.Entity;
import org.biopax.paxtools.model.level3.EntityReference;
import org.biopax.paxtools.model.level3.Gene;
import org.biopax.paxtools.model.level3.GeneticInteraction;
@@ -359,15 +360,22 @@
}
/**
- * Convert SBML Species to BioPAX Physical Entity
+ * Convert SBML Species to BioPAX Entity
*
- * @param bpModel - The BioPAX Model to store the Physical Entity that was converted from the given SBML Species.
- * @param species - The SBML Species to be converted to a BioPAX Physical Entities
+ * @param bpModel - The BioPAX Model to store the Entity that was converted from the given SBML Species.
+ * @param species - The SBML Species to be converted to a BioPAX Entities
* @return The converted BioPAX Physical Entity
*/
- public PhysicalEntity convertSpecies(Model bpModel, Species species) {
- PhysicalEntity physicalEntity;
+ public Entity convertSpecies(Model bpModel, Species species) {
+ PhysicalEntity physicalEntity = null;
+ Entity entity = null;
+ boolean isPhysicalEntity = true;
+
switch (species.getSBOTerm()) {
+ case 243: //Gene
+ entity = convertGeneFromSpecies(bpModel, species);
+ isPhysicalEntity = false;
+ break;
case 253: // Complex
physicalEntity = createComplexFromSpecies(bpModel, species);
break;
@@ -392,9 +400,14 @@
break;
}
+ if(!isPhysicalEntity){
+ return entity;
+ }
+
CellularLocationVocabulary cellularLocationVocabulary = createCompartment(bpModel, species.getCompartmentInstance());
physicalEntity.setCellularLocation(cellularLocationVocabulary);
-
+
+
return physicalEntity;
}
@@ -443,7 +456,7 @@
* @param species - The SBML Species to be converted to a BioPAX Gene Entity
* @return The converted BioPAX Gene
*/
- public Gene createGeneFromSpecies(Model bpModel, Species species) {
+ public Gene convertGeneFromSpecies(Model bpModel, Species species) {
Gene gene = createBPEfromSBMLE(bpModel, Gene.class, species);
for (Xref xref : generateXrefsForSBase(bpModel, UnificationXref.class, species)) {
gene.addXref(xref);
Modified: trunk/test/org/sbfc/test/biopax2sbml/InteractionTests.java
===================================================================
--- trunk/test/org/sbfc/test/biopax2sbml/InteractionTests.java 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/test/org/sbfc/test/biopax2sbml/InteractionTests.java 2016-07-15 07:14:10 UTC (rev 673)
@@ -297,7 +297,7 @@
return biopax2sbmlModel;
}
- public void printSBMLModel(SBMLModel sbfcSBMLModel)
+ public static void printSBMLModel(SBMLModel sbfcSBMLModel)
{
try
{
@@ -459,7 +459,7 @@
SBMLModel sbfcSBMLModel = read_biopaxFile(owlFile);
org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- //printSBMLModel(sbfcSBMLModel);
+// printSBMLModel(sbfcSBMLModel);
}
@Test public void test_TemplateReactionFile()
Modified: trunk/test/org/sbfc/test/biopax2sbml/PhysicalEntityTests.java
===================================================================
--- trunk/test/org/sbfc/test/biopax2sbml/PhysicalEntityTests.java 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/test/org/sbfc/test/biopax2sbml/PhysicalEntityTests.java 2016-07-15 07:14:10 UTC (rev 673)
@@ -25,10 +25,13 @@
import org.sbfc.converter.exceptions.ReadModelException;
import org.sbfc.converter.models.BioPAXModel;
import org.sbfc.converter.models.SBMLModel;
+import org.sbml.jsbml.ModifierSpeciesReference;
+import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBO;
import org.sbml.jsbml.Species;
+import org.sbml.jsbml.CVTerm.Qualifier;
/**
@@ -280,6 +283,45 @@
SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+
+ assert(sbmlModel.getModel().getId().equals("defaultSBMLModelId"));
+ assert(sbmlModel.getNumSpecies() == 2);
+ assert(sbmlModel.getNumReactions() == 1);
+
+ assert(sbmlModel.getNumModifierSpeciesReferences() == 2);
+
+ for(ModifierSpeciesReference modifier : sbmlModel.getModifierSpeciesReferences())
+ {
+ if(modifier.getSpecies().equals("Gene_1") || modifier.getSpecies().equals("Gene_3"))
+ {
+ assert(true);
+ }
+ }
+
+ assert(sbmlModel.containsSpecies("Gene_1"));
+ Species gene1 = sbmlModel.getSpecies("Gene_1");
+ assert(gene1.getName().equals("MLC1"));
+ assert(gene1.getSBOTerm() == SBO.getGene());
+ assert(gene1.getCVTermCount() == 1);
+ assert(gene1.getCVTerms().iterator().next().getBiologicalQualifierType().equals(Qualifier.BQB_IS));
+
+ assert(sbmlModel.containsSpecies("Gene_3"));
+ Species gene3 = sbmlModel.getSpecies("Gene_3");
+ assert(gene3.getName().equals("MYO2"));
+ assert(gene3.getSBOTerm() == SBO.getGene());
+ assert(gene3.getCVTerms().iterator().next().getBiologicalQualifierType().equals(Qualifier.BQB_IS));
+ assert(gene3.getCVTerms().iterator().next().getResources().size() == 1);
+
+
+ assert(sbmlModel.containsReaction("GeneticInteraction_2"));
+ Reaction GeneticInteraction_2 = sbmlModel.getReaction("GeneticInteraction_2");
+ assert(GeneticInteraction_2.getName().equals("MYO2 - MLC1"));
+ assert(GeneticInteraction_2.getSBOTerm() == SBO.getGeneticInteraction());
+ assert(GeneticInteraction_2.getCVTerms().iterator().next().getBiologicalQualifierType().equals(Qualifier.BQB_IS_DESCRIBED_BY));
+ assert(GeneticInteraction_2.getCVTerms().size() == 2);
+ assert(GeneticInteraction_2.getCVTerms().iterator().next().getResources().size() == 1);
+// InteractionTests.printSBMLModel(sbfcSBMLModel);
+
}
@Test public void test_ComplexFile()
@@ -290,43 +332,43 @@
org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
}
- @Test public void test_ProteinFile()
- {
- String owlFile = InteractionTests.fileDirectory + "biopax3-phosphorylation-reaction.owl";
-
- SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
- org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- }
-
- @Test public void test_DnaFile()
- {
- String owlFile = InteractionTests.fileDirectory + "circadian_clock.owl";
-
- SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
- org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- }
-
- @Test public void test_DnaRegionFile()
- {
- String owlFile = InteractionTests.fileDirectory + "biopax3-template-reaction.owl";
-
- SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
- org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- }
-
- @Test public void test_RnaFile()
- {
- String owlFile = InteractionTests.fileDirectory + "testBiochemReactParticipantsLocationRule_Transport.owl";
-
- SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
- org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- }
-
- @Test public void test_SmallMoleculeFile()
- {
- String owlFile = InteractionTests.fileDirectory + "biopax3-phosphorylation-reaction.owl";
-
- SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
- org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
- }
+// @Test public void test_ProteinFile()
+// {
+// String owlFile = InteractionTests.fileDirectory + "biopax3-phosphorylation-reaction.owl";
+//
+// SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
+// org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+// }
+//
+// @Test public void test_DnaFile()
+// {
+// String owlFile = InteractionTests.fileDirectory + "circadian_clock.owl";
+//
+// SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
+// org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+// }
+//
+// @Test public void test_DnaRegionFile()
+// {
+// String owlFile = InteractionTests.fileDirectory + "biopax3-template-reaction.owl";
+//
+// SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
+// org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+// }
+//
+// @Test public void test_RnaFile()
+// {
+// String owlFile = InteractionTests.fileDirectory + "testBiochemReactParticipantsLocationRule_Transport.owl";
+//
+// SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
+// org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+// }
+//
+// @Test public void test_SmallMoleculeFile()
+// {
+// String owlFile = InteractionTests.fileDirectory + "biopax3-phosphorylation-reaction.owl";
+//
+// SBMLModel sbfcSBMLModel = InteractionTests.read_biopaxFile(owlFile);
+// org.sbml.jsbml.Model sbmlModel = sbfcSBMLModel.getModel();
+// }
}
Added: trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-genetic-interaction.xml
===================================================================
--- trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-genetic-interaction.xml (rev 0)
+++ trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-genetic-interaction.xml 2016-07-15 07:14:10 UTC (rev 673)
@@ -0,0 +1,87 @@
+<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="defaultSBMLModelId" metaid="b76502ad-7c4a-4417-a6ad-25075b1d82a6" substanceUnits="substance" timeUnits="time" volumeUnits="volume">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <p>This model has been automatically generated by BioPAX2SBML</p>
+ </body>
+ </notes>
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
+ <rdf:Description rdf:about="#b76502ad-7c4a-4417-a6ad-25075b1d82a6">
+ <dc:creator>
+ <rdf:Bag>
+ <rdf:li rdf:parseType="Resource">
+ <vCard:ORG rdf:parseType="Resource">
+ <vCard:Orgname>GSoC 2016, National Resource for Network Biology</vCard:Orgname>
+ </vCard:ORG>
+ </rdf:li>
+ </rdf:Bag>
+ </dc:creator>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfCompartments>
+ <compartment constant="true" id="default" sboTerm="SBO:0000290" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="true" id="Gene_1" metaid="_29f5b0ac-cbaf-4220-b7e9-f8b0a846ebe2" name="MLC1"
+ sboTerm="SBO:0000243">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#_29f5b0ac-cbaf-4220-b7e9-f8b0a846ebe2">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/852772" />
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="true" id="Gene_3" metaid="c7959c83-e60c-4346-93dc-0f3a087b9f4b" name="MYO2"
+ sboTerm="SBO:0000243">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#c7959c83-e60c-4346-93dc-0f3a087b9f4b">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/ncbigene/854504" />
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction fast="false" id="GeneticInteraction_2" metaid="_06543bdd-4aaa-4350-9860-463a7d528c3e" name="MYO2 - MLC1" reversible="false" sboTerm="SBO:0000343">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#_06543bdd-4aaa-4350-9860-463a7d528c3e">
+ <bqbiol:unknownQualifier>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://www.biopax.org/examples/myExample#Evidence_4" />
+ <bqbiol:unknownQualifier>
+ <rdf:Bag>
+ <rdf:li rdf:resource="MI:0441" />
+ </rdf:Bag>
+ </bqbiol:unknownQualifier>
+ </rdf:Bag>
+ </bqbiol:unknownQualifier>
+ <bqbiol:isDescribedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/pubmed/9700160" />
+ </rdf:Bag>
+ </bqbiol:isDescribedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfModifiers>
+ <modifierSpeciesReference species="Gene_1" />
+ <modifierSpeciesReference species="Gene_3" />
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Modified: trunk/test/org/sbfc/test/resources/biopax3-template-reaction.owl
===================================================================
--- trunk/test/org/sbfc/test/resources/biopax3-template-reaction.owl 2016-07-14 18:47:55 UTC (rev 672)
+++ trunk/test/org/sbfc/test/resources/biopax3-template-reaction.owl 2016-07-15 07:14:10 UTC (rev 673)
@@ -101,6 +101,7 @@
>TCF1_protein_ref</bp:displayName>
<bp:xref rdf:resource="#PublicationXref_11"/>
<bp:xref rdf:resource="#PublicationXref_10"/>
+ <bp:xref rdf:resource="#UnificationXref_8"/>
</bp:ProteinReference>
</bp:entityReference>
<bp:cellularLocation rdf:resource="#CellularLocationVocabulary_3"/>
Added: trunk/test/org/sbfc/test/sbml2biopax/outputFiles/biopax3-genetic-interaction.owl
===================================================================
--- trunk/test/org/sbfc/test/sbml2biopax/outputFiles/biopax3-genetic-interaction.owl (rev 0)
+++ trunk/test/org/sbfc/test/sbml2biopax/outputFiles/biopax3-genetic-interaction.owl 2016-07-15 07:14:10 UTC (rev 673)
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"
+ xml:base="http://www.humanmetabolism.org/#">
+<owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
+</owl:Ontology>
+
+<bp:Pathway rdf:ID="defaultSBMLModelId">
+ <bp:pathwayComponent rdf:resource="#GeneticInteraction_2" />
+ <bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string"></bp:standardName>
+ <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string"></bp:displayName>
+ <bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">
+
+ This model has been automatically generated by BioPAX2SBML
+
+ </bp:comment>
+</bp:Pathway>
+
+<bp:Gene rdf:ID="Gene_3">
+ <bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MYO2</bp:standardName>
+ <bp:xref rdf:resource="#unificationxref_156418227" />
+ <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MYO2</bp:displayName>
+</bp:Gene>
+
+<bp:PublicationXref rdf:ID="relationshipxref_609196062">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">9700160</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">PubMed</bp:db>
+</bp:PublicationXref>
+
+<bp:BioSource rdf:ID="source_human">
+ <bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Homo sapiens</bp:standardName>
+ <bp:xref rdf:resource="#xref_human_tax" />
+ <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Homo sapiens</bp:displayName>
+</bp:BioSource>
+
+<bp:GeneticInteraction rdf:ID="GeneticInteraction_2">
+ <bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MYO2 - MLC1</bp:standardName>
+ <bp:xref rdf:resource="#relationshipxref_609196062" />
+ <bp:xref rdf:resource="#relationshipxref_1259900386" />
+ <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MYO2 - MLC1</bp:displayName>
+ <bp:participant rdf:resource="#Gene_3" />
+ <bp:participant rdf:resource="#Gene_1" />
+</bp:GeneticInteraction>
+
+<bp:UnificationXref rdf:ID="unificationxref_156418227">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">854504</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">NCBI Gene</bp:db>
+</bp:UnificationXref>
+
+<bp:RelationshipXref rdf:ID="relxref_biomodels">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MODEL1109130000</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">BioModels</bp:db>
+</bp:RelationshipXref>
+
+<bp:UnificationXref rdf:ID="unificationxref_108853767">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">852772</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">NCBI Gene</bp:db>
+</bp:UnificationXref>
+
+<bp:Gene rdf:ID="Gene_1">
+ <bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MLC1</bp:standardName>
+ <bp:xref rdf:resource="#unificationxref_108853767" />
+ <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MLC1</bp:displayName>
+</bp:Gene>
+
+<bp:RelationshipXref rdf:ID="relationshipxref_1259900386">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Evidence_4</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">http://www.biopax.org/examples/myExample</bp:db>
+</bp:RelationshipXref>
+
+<bp:UnificationXref rdf:ID="xref_human_tax">
+ <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">9606</bp:id>
+ <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">taxonomy</bp:db>
+</bp:UnificationXref>
+</rdf:RDF>
\ No newline at end of file
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