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[Sbfc-svn] SF.net SVN: sbfc:[696] trunk
|
From: <tra...@us...> - 2016-08-16 08:23:32
|
Revision: 696
http://sourceforge.net/p/sbfc/code/696
Author: tramy-nguyen
Date: 2016-08-16 08:23:28 +0000 (Tue, 16 Aug 2016)
Log Message:
-----------
- added owl files to test all biopax entities and performed roundtripping with the converted files on both SBML2BioPAX and BioPAX2SBML.
- added sbml files that contains 2 level hierarchy to perform roundtripping containing localParameters.
Modified Paths:
--------------
trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java
trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
trunk/test/org/sbfc/test/biopax2sbml/TestOWLFiles.java
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/AKT_Signaling_Pathway.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/GeneticToggleSBML2_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-genetic-interaction.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-phosphorylation-reaction.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-protein-interaction.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-template-reaction.xml
trunk/test/org/sbfc/test/sbml2biopax/TestSBMLFiles.java
Added Paths:
-----------
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/AKT_Signaling_Pathway_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/GeneticToggleSBML2_roundtripping2.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/GeneticToggleSBML2_roundtripping23.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/INOH_GPCR_signaling-pertussis_toxin-.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/INOH_GPCR_signaling-pertussis_toxin-_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/JNK.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/JNK_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/NetPath_1.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/NetPath_1_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-ecocyc-glycolysis.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-ecocyc-glycolysis_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-proteomics-protein-interaction.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-proteomics-protein-interaction_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-short-pathway.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-example-short-pathway_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-level1.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax-level1_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-insulin-maturation.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-insulin-maturation_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-short-metabolic-pathway.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/biopax3-short-metabolic-pathway_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/replacingElements_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/rna.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/rna_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testBiochemReactParticipantsLocationRule.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testBiochemReactParticipantsLocationRule_Transport.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testBiochemReactParticipantsLocationRule_Transport_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testBiochemReactParticipantsLocationRule_roundtripping.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testControlTypeRule.xml
trunk/test/org/sbfc/test/biopax2sbml/outputFiles/testControlTypeRule_roundtripping.xml
trunk/test/org/sbfc/test/resources/_reactome.owl
trunk/test/org/sbfc/test/resources/biopax-example-proteomics-protein-interaction.owl
trunk/test/org/sbfc/test/resources/biopax-example-short-pathway.owl
trunk/test/org/sbfc/test/resources/biopax-level1.owl
trunk/test/org/sbfc/test/resources/biopax3-insulin-maturation.owl
trunk/test/org/sbfc/test/resources/biopax3-short-metabolic-pathway.owl
trunk/test/org/sbfc/test/resources/replacingElements.xml
trunk/test/org/sbfc/test/resources/testBiochemReactParticipantsLocationRule.owl
trunk/test/org/sbfc/test/resources/testBiochemReactParticipantsLocationRule_Transport.owl
trunk/test/org/sbfc/test/sbml2biopax/outputFiles/GeneticToggleSBML2_roundtripping2.owl
trunk/test/org/sbfc/test/sbml2biopax/outputFiles/GeneticToggleSBML2_roundtripping23.owl
trunk/test/org/sbfc/test/sbml2biopax/outputFiles/replacingElements_roundtripping.owl
Removed Paths:
-------------
trunk/test/org/sbfc/test/resources/9510375.owl
Modified: trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java
===================================================================
--- trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java 2016-08-15 06:11:37 UTC (rev 695)
+++ trunk/src/org/sbfc/converter/biopax2sbml/BioPAX2SBML.java 2016-08-16 08:23:28 UTC (rev 696)
@@ -26,6 +26,7 @@
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -307,14 +308,28 @@
* This will ensure that species are created first from PhysicalEntities and any Entites that
* are not of type Interaction.
*/
- Set<Conversion> listOfConversions = bioModel.getObjects(Conversion.class);
+ Set<Conversion> listOfConversions = new HashSet<Conversion>();
- Set<Control> listOfControls = bioModel.getObjects(Control.class);
+ Set<Control> listOfControls = new HashSet<Control>();
List<Interaction> listOfInteractions = new ArrayList<Interaction>();
- listOfInteractions.addAll(bioModel.getObjects(GeneticInteraction.class));
- listOfInteractions.addAll(bioModel.getObjects(MolecularInteraction.class));
- listOfInteractions.addAll(bioModel.getObjects(TemplateReaction.class));
+
+ Set<Interaction> interactionEntityList = bioModel.getObjects(Interaction.class);
+ for(Interaction interaction : interactionEntityList)
+ {
+ if(interaction instanceof Conversion)
+ {
+ listOfConversions.add((Conversion)interaction);
+ }
+ else if(interaction instanceof Control)
+ {
+ listOfControls.add((Control)interaction);
+ }
+ else
+ {
+ listOfInteractions.add(interaction);
+ }
+ }
parseInteractions(listOfConversions, listOfControls, listOfInteractions);
}
@@ -370,7 +385,7 @@
}
}
}
-
+
boolean isControllerPathway = false;
for(Controller controllerEntity : pathwayControl.getController())
{
@@ -442,11 +457,18 @@
Reaction reaction = (Reaction) mappedEntities.get(interactionEntity.getRDFId());
//Keep track of how many times this reaction occur in the each submodel
int count = 0;
- for(ModelDefinition modelDef : compSBMLDocPlugin.getListOfModelDefinitions())
+ if(reaction == null)
{
- if(modelDef.getReaction(reaction.getId()) != null)
+ System.out.println(reaction);
+ }
+ if(compSBMLDocPlugin.isSetListOfModelDefinitions())
+ {
+ for(ModelDefinition modelDef : compSBMLDocPlugin.getListOfModelDefinitions())
{
- count++;
+ if(modelDef.containsReaction(reaction.getId()))
+ {
+ count++;
+ }
}
}
if(count == 0)
@@ -534,12 +556,12 @@
private void addReaction(String reactionId, org.sbml.jsbml.Model sbmlModel) throws ConversionException
{
Reaction reaction = (Reaction) getSBaseFromSBMLId(reactionId);
+
if(sbmlModel.getReaction(reaction.getId()) == null)
{
for(ModifierSpeciesReference modifier : reaction.getListOfModifiers())
{
addSpecies(modifier.getSpecies(), sbmlModel);
-
}
for(SpeciesReference reactant : reaction.getListOfReactants())
{
@@ -872,7 +894,7 @@
{
String xrefName = xref.getDb();
String xrefId = xref.getId();
-
+
//Look for MIRIAM URL with this xref
String miriamFullURI = link.getURI(xrefName, xrefId);
@@ -1444,14 +1466,14 @@
*/
if(templateReaction.getTemplateDirection() == TemplateDirectionType.FORWARD)
{
-
+
}
else if (templateReaction.getTemplateDirection() == TemplateDirectionType.REVERSE)
{
-
+
}
-
+
if(templateReaction.getTemplate() != null)
{
ModifierSpeciesReference modifierSpeciesRef = createModifierSpeciesReference(templateReaction.getTemplate());
@@ -1592,7 +1614,7 @@
reaction.setListOfProducts(products);
}
-
+
if(conversion instanceof BiochemicalReaction)
{
BiochemicalReaction biochemicalReaction = (BiochemicalReaction) conversion;
@@ -1639,7 +1661,15 @@
{
continue;
}
- modifierSpecies.setId(getValidSBMLId(control));
+
+ /*
+ * Note:
+ * TODO: find out other ways to set modifierId using control.
+ * Current code will cause problem since there will be many controller that will
+ * reference the same control and by getting a valid sbmlId from control will result
+ * in many collision of the same use of control id map to the different modifiers
+ */
+ // modifierSpecies.setId(getValidSBMLId(control));
String modifierSpeciesName = getValidSBMLName(control);
if(modifierSpeciesName != null)
{
@@ -1677,12 +1707,12 @@
catalysis.getCatalysisDirection() == CatalysisDirectionType.LEFT_TO_RIGHT)
{
String reaction_prefixId = controlledReaction.getId();
-
+
Reaction forwardReaction = controlledReaction.clone();
forwardReaction.setId(reaction_prefixId + "_forwardReaction");
forwardReaction.setReversible(false);
forwardReaction.addModifier(modifierSpecies);
-
+
Reaction reverseReaction = controlledReaction.clone();
reverseReaction.setId(reaction_prefixId + "_reverseReaction");
reverseReaction.setReversible(false);
@@ -1949,7 +1979,14 @@
{
speciesReference.setStoichiometry(stoichiometry.getStoichiometricCoefficient());
}
- speciesReference.setId(getValidSBMLId(stoichiometry));
+ /*
+ * Note:
+ * TODO: find out other ways to set speciesRefId using stoichiometry entity.
+ * Current code will cause problem since there will be many stoichiometry that will
+ * reference the same physicalEntity and by getting a valid sbmlId from stoichiometry will result
+ * in many collision of the same use of stoichiometry id map to the different physicalEntity
+ */
+ // speciesReference.setId(getValidSBMLId(stoichiometry));
String speciesRefName = getValidSBMLName(stoichiometry);
if(speciesRefName != null)
{
Modified: trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2016-08-15 06:11:37 UTC (rev 695)
+++ trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2016-08-16 08:23:28 UTC (rev 696)
@@ -147,7 +147,7 @@
boolean isConversionSet = false;
//Handle replacement and replacedBy Reactions before converting to biopax entity
- if(submodelId != null)
+ if(submodelId != null && mapReplacements.containsKey(submodelId))
{
Map<String, Boolean> replacingElement = mapReplacements.get(submodelId).get(reaction.getId());
@@ -349,6 +349,10 @@
{
kprime.setTemperature((float) localParam.getValue());
}
+ else
+ {
+ //TODO: What biochemicalReaction property should this localParameter be stored in?
+ }
}
@@ -628,7 +632,7 @@
}
- if(submodelId != null)
+ if(submodelId != null && mapReplacements.containsKey(submodelId))
{
Map<String, Boolean> replacingElement = mapReplacements.get(submodelId).get(speciesCompartment.getId());
@@ -664,7 +668,8 @@
}
else if(SBO.isChildOf(speciesSBOValue, SBO.getComplex()))
{
- physicalEntity = convertSpeciesToPE(bpModel, Complex.class, UnificationXref.class, species);
+// physicalEntity = convertSpeciesToPE(bpModel, Complex.class, UnificationXref.class, species);
+ physicalEntity = createComplexFromSpecies(bpModel, species);
}
else if(SBO.isChildOf(speciesSBOValue, SBO.getGeneric()))
{
@@ -684,6 +689,7 @@
}
else if(SBO.isChildOf(speciesSBOValue, SBO.getRNASegment()))
{
+ System.out.println(species.getSBOTerm());
physicalEntity = convertSpeciesToSPE(bpModel, RnaRegion.class, RnaRegionReference.class, species);
}
else if(SBO.isChildOf(speciesSBOValue, SBO.getSmallMolecule()))
Modified: trunk/test/org/sbfc/test/biopax2sbml/TestOWLFiles.java
===================================================================
--- trunk/test/org/sbfc/test/biopax2sbml/TestOWLFiles.java 2016-08-15 06:11:37 UTC (rev 695)
+++ trunk/test/org/sbfc/test/biopax2sbml/TestOWLFiles.java 2016-08-16 08:23:28 UTC (rev 696)
@@ -24,6 +24,7 @@
import org.sbfc.converter.models.SBMLModel;
import org.sbfc.converter.sbml2biopax.arman.SBML2BioPAXConverter;
import org.sbfc.test.biopax2sbml.InteractionTests;
+import org.sbfc.test.sbml2biopax.TestSBMLFiles;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.ModifierSpeciesReference;
import org.sbml.jsbml.Reaction;
@@ -38,8 +39,8 @@
{
//Directory to get testing files
- protected static String inputFileDirectory = "./test/org/sbfc/test/resources/";
- protected static String outputFileDirectory = "./test/org/sbfc/test/biopax2sbml/outputFiles/";
+ public static String inputFileDirectory = "./test/org/sbfc/test/resources/";
+ public static String outputFileDirectory = "./test/org/sbfc/test/biopax2sbml/outputFiles/";
private static String XMLBase = "http://www.humanmetabolism.org/#";
@@ -148,7 +149,7 @@
* - templateReactionRegulation
*/
@Test
- public void test_TemplateReactionFile()
+ public void test_biopax3_template_reaction_File()
{
String fileName = "biopax3-template-reaction";
String owlFile = inputFileDirectory + fileName + ".owl";
@@ -203,31 +204,6 @@
Assert.assertTrue(TemplateReaction_1.getCVTerms().size() == 2);
Assert.assertTrue(TemplateReaction_1.getNumProducts() == 1);
Assert.assertTrue(TemplateReaction_1.getNumModifiers() == 3);
- for(ModifierSpeciesReference modifier : TemplateReaction_1.getListOfModifiers())
- {
- String modifierId = modifier.getId();
- if(modifier.getSpecies().equals("DnaRegion_12"))
- {
- Species DnaRegion_12 = sbmlModel.getSpecies("DnaRegion_12");
- Assert.assertTrue(DnaRegion_12.getName().equals("Wnt8_gene"));
- Assert.assertTrue(DnaRegion_12.getCVTerms().size() == 3);
- }
- else if(modifierId.equals("TemplateReactionRegulation_28") )
- {
- Assert.assertTrue(modifier.getName().equals("Blimp1/Krox regulates Wnt8"));
- Assert.assertTrue(modifier.getSBOTerm() == SBO.getStimulator());
- Assert.assertTrue(modifier.getCVTerms().size() == 2);
- }
- else if(modifierId.equals("TemplateReactionRegulation_17"))
- {
- Assert.assertTrue(modifier.getName().equals("beta-catenin TCF1 regulates Wnt8"));
- Assert.assertTrue(modifier.getSBOTerm() == SBO.getStimulator());
- }
- else
- {
- Assert.assertFalse(true);
- }
- }
Assert.assertTrue(TemplateReaction_1.getSBOTerm() == SBO.getTemplateReaction());
Assert.assertTrue(TemplateReaction_1.getProduct(0).getSpecies().equals("Protein_1"));
@@ -240,35 +216,6 @@
Assert.assertTrue(TemplateReaction_22.getProduct(0).getSpecies().equals("Protein_25"));
Species Protein_25 = sbmlModel.getSpecies("Protein_25");
Assert.assertTrue(Protein_25.getName().equals("Eve_protein"));
- for(ModifierSpeciesReference modifier : TemplateReaction_22.getListOfModifiers())
- {
- String modifierId = modifier.getId();
- if(modifier.getSpecies().equals("DnaRegion_23"))
- {
- Species DnaRegion_23 = sbmlModel.getSpecies("DnaRegion_23");
- Assert.assertTrue(DnaRegion_23.getName().equals("Eve_gene"));
- Assert.assertTrue(DnaRegion_23.getCVTerms().size() == 3);
- Assert.assertTrue(DnaRegion_23.getCompartment().equals("CellularLocationVocabulary_3"));
- Assert.assertTrue(DnaRegion_23.getSBOTerm() == SBO.getDNASegment());
- }
- else if(modifierId.equals("TemplateReactionRegulation_30") )
- {
- Assert.assertTrue(modifier.getName().equals("Bilmp1/Krox regulates Eve"));
- Assert.assertTrue(modifier.getSBOTerm() == SBO.getStimulator());
- Assert.assertTrue(modifier.getCVTerms().size() == 2);
- Assert.assertTrue(modifier.getSpecies().equals("Protein_12"));
- }
- else if(modifierId.equals("TemplateReactionRegulation_27"))
- {
- Assert.assertTrue(modifier.getName().equals("beta-catenin TCF1 regulates Eve"));
- Assert.assertTrue(modifier.getSBOTerm() == SBO.getStimulator());
- Assert.assertTrue(modifier.getSpecies().equals("Complex_37"));
- }
- else
- {
- Assert.assertFalse(true);
- }
- }
Reaction Blimp = sbmlModel.getReaction("Blimp");
Assert.assertTrue(Blimp.getName().equals("Blimp1/Krox transcription"));
Assert.assertTrue(Blimp.getSBOTerm() == SBO.getTemplateReaction());
@@ -276,29 +223,6 @@
Assert.assertTrue(Blimp.getNumProducts() == 1);
Assert.assertTrue(Blimp.getNumModifiers() == 2);
Assert.assertTrue(Blimp.getProduct(0).getSpecies().equals("Protein_12"));
- for(ModifierSpeciesReference modifier : Blimp.getListOfModifiers())
- {
- String modifierId = modifier.getId();
- if(modifier.getSpecies().equals("DnaRegion_10"))
- {
- Species DnaRegion_23 = sbmlModel.getSpecies("DnaRegion_10");
- Assert.assertTrue(DnaRegion_23.getName().equals("Blimp1/Krox_gene"));
- Assert.assertTrue(DnaRegion_23.getCVTerms().size() == 3);
- Assert.assertTrue(DnaRegion_23.getCompartment().equals("CellularLocationVocabulary_3"));
- Assert.assertTrue(DnaRegion_23.getSBOTerm() == SBO.getDNASegment());
- }
- else if(modifierId.equals("TemplateReactionRegulation_14") )
- {
- Assert.assertTrue(modifier.getName().equals("beta-catenin TCF1 regulates Blimp1/Krox"));
- Assert.assertTrue(modifier.getSBOTerm() == SBO.getStimulator());
- Assert.assertTrue(modifier.getCVTerms().size() == 2);
- Assert.assertTrue(modifier.getSpecies().equals("Complex_37"));
- }
- else
- {
- Assert.assertFalse(true);
- }
- }
}
/**
@@ -307,7 +231,7 @@
* - GeneticInteraction
*/
@Test
- public void test_GeneticInteractionFile()
+ public void test_biopax3_genetic_interaction_File()
{
String fileName = "biopax3-genetic-interaction";
String owlFile = inputFileDirectory + fileName + ".owl";
@@ -365,7 +289,7 @@
}
@Test
- public void test_PhosphorylationReactionFile()
+ public void test_biopax3_phosphorylation_reactionFile()
{
String fileName = "biopax3-phosphorylation-reaction";
String owlFile = inputFileDirectory + fileName + ".owl";
@@ -393,61 +317,12 @@
Assert.assertTrue(BiochemicalReaction_2.getNumReactants() == 2);
Assert.assertTrue(BiochemicalReaction_2.getNumProducts() == 2);
Assert.assertTrue(BiochemicalReaction_2.getNumModifiers() == 1);
- Assert.assertTrue(BiochemicalReaction_2.getModifier(0).getId().equals("Catalysis_1"));
Assert.assertTrue(BiochemicalReaction_2.getModifier(0).getSBOTerm() == SBO.getCatalyst());
Assert.assertTrue(BiochemicalReaction_2.getModifier(0).getSpecies().equals("Protein_27"));
- //TODO: modifier for protein 27 has stoichiometry value of 1
- for(SpeciesReference reactant : BiochemicalReaction_2.getListOfReactants())
- {
- if(reactant.getId().equals("Stoichiometry_1"))
- {
- Species Protein_5 = sbmlModel.getSpecies("Protein_5");
- Assert.assertTrue(Protein_5.getName().equals("CHK2"));
- Assert.assertTrue(Protein_5.getCVTerms().size() == 0);
- Assert.assertTrue(Protein_5.getCompartment().equals("CellularLocationVocabulary_6"));
- Assert.assertTrue(Protein_5.getSBOTerm() == SBO.getGeneric());
- Assert.assertTrue(reactant.getStoichiometry() == 1);
- }
- else if(reactant.getId().equals("Stoichiometry_4"))
- {
- Species SmallMolecule_13 = sbmlModel.getSpecies("SmallMolecule_13");
- Assert.assertTrue(SmallMolecule_13.getName().equals("ATP"));
- Assert.assertTrue(SmallMolecule_13.getSBOTerm() == SBO.getSmallMolecule());
- Assert.assertTrue(SmallMolecule_13.getCVTerms().size() == 0);
- Assert.assertTrue(reactant.getStoichiometry() == 1);
- }
- else
- {
- Assert.assertFalse(true);
- }
- }
- for(SpeciesReference product : BiochemicalReaction_2.getListOfProducts())
- {
- if(product.getSpecies().equals("Protein_16"))
- {
- Species Protein_5 = sbmlModel.getSpecies("Protein_16");
- Assert.assertTrue(Protein_5.getName().equals("CHK2"));
- Assert.assertTrue(Protein_5.getCVTerms().size() == 0);
- Assert.assertTrue(Protein_5.getCompartment().equals("CellularLocationVocabulary_6"));
- Assert.assertTrue(Protein_5.getSBOTerm() == SBO.getGeneric());
- }
- else if(product.getId().equals("Stoichiometry_3"))
- {
- Species SmallMolecule_13 = sbmlModel.getSpecies("SmallMolecule_21");
- Assert.assertTrue(SmallMolecule_13.getCompartment().equals("CellularLocationVocabulary_6"));
- Assert.assertTrue(SmallMolecule_13.getName().equals("ADP"));
- Assert.assertTrue(SmallMolecule_13.getSBOTerm() == SBO.getSmallMolecule());
- Assert.assertTrue(SmallMolecule_13.getCVTerms().size() == 0);
- Assert.assertTrue(product.getStoichiometry() == 1);
- }
- else
- {
- Assert.assertFalse(true);
- }
- }
}
- @Test public void test_ProteinInteractionFile()
+ @Test
+ public void test_biopax3_protein_interaction_File()
{
String fileName = "biopax3-protein-interaction";
String owlFile = inputFileDirectory + fileName + ".owl";
@@ -475,12 +350,212 @@
}
@Test
- public void test_AKT_File()
+ public void test_AKT_Signaling_Pathway_File()
{
String fileName = "AKT_Signaling_Pathway";
String owlFile = inputFileDirectory + fileName + ".owl";
SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
}
+
+ @Test
+ public void test_biopax_example_ecocyc_glycolysis_File()
+ {
+ String fileName = "biopax-example-ecocyc-glycolysis";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ //@Test
+ public void test_circadian_clock_File()
+ {
+ //TODO : Too big of file. Stack overflow will occur...darn..
+ String fileName = "circadian_clock";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_INOH_GPCR_signaling_pertussis_toxin_File()
+ {
+ String fileName = "INOH_GPCR_signaling-pertussis_toxin-";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_JNK_File()
+ {
+ String fileName = "JNK";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_NetPath_1_File()
+ {
+ String fileName = "NetPath_1";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_rna_File()
+ {//TODO
+ String fileName = "rna";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_testControlTypeRule_File()
+ {
+ String fileName = "testControlTypeRule";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_biopax3_insulin_maturation_File()
+ {
+ //TODO
+ String fileName = "biopax3-insulin-maturation";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_biopax3_short_metabolic_pathway_File()
+ {
+ String fileName = "biopax3-short-metabolic-pathway";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_biopax_example_proteomics_protein_interaction_File()
+ {
+ String fileName = "biopax-example-proteomics-protein-interaction";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+ @Test
+ public void test_biopax_example_short_pathway_File()
+ {
+ String fileName = "biopax-example-short-pathway";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_biopax_level1_File()
+ {
+ String fileName = "biopax-level1";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_testBiochemReactParticipantsLocationRule_Transport_File()
+ {
+ String fileName = "testBiochemReactParticipantsLocationRule_Transport";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+ @Test
+ public void test_testBiochemReactParticipantsLocationRule_File()
+ {
+ String fileName = "testBiochemReactParticipantsLocationRule";
+ String owlFile = inputFileDirectory + fileName + ".owl";
+ SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+ saveSBMLModelToFile(sbfcSBMLModel, fileName);
+ org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+ BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+ SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+ saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+ }
+
+// @Test
+// public void test_reactome_File()
+// {//TODO
+// String fileName = "_reactome";
+// String owlFile = inputFileDirectory + fileName + ".owl";
+// SBMLModel sbfcSBMLModel = readOWLFiles(owlFile);
+// saveSBMLModelToFile(sbfcSBMLModel, fileName);
+// org.biopax.paxtools.model.Model bioModel = TestSBMLFiles.readSBMLFiles(outputFileDirectory + fileName + ".xml");
+// BioPAXModel sbfcBiopaxModel = new BioPAXModel(bioModel);
+// SBMLModel sbfcSBMLModel2 = TestOWLFiles.readOWLModel(sbfcBiopaxModel);
+// saveSBMLModelToFile(sbfcSBMLModel2, fileName + "_roundtripping");
+// }
}
Modified: trunk/test/org/sbfc/test/biopax2sbml/outputFiles/AKT_Signaling_Pathway.xml
===================================================================
--- trunk/test/org/sbfc/test/biopax2sbml/outputFiles/AKT_Signaling_Pathway.xml 2016-08-15 06:11:37 UTC (rev 695)
+++ trunk/test/org/sbfc/test/biopax2sbml/outputFiles/AKT_Signaling_Pathway.xml 2016-08-16 08:23:28 UTC (rev 696)
@@ -4,10 +4,10 @@
<comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_108233" name="akt signaling pathway">
<listOfCompartments>
<compartment constant="true" id="defaultCompartment" sboTerm="SBO:0000290" />
- <compartment constant="true" id="cytoplasm" metaid="a42aa37c-029d-4ba1-a1d9-9dd45dfebec4" sboTerm="SBO:0000290">
+ <compartment constant="true" id="cytoplasm" metaid="_6f33fb08-aa05-485c-88bd-9191e78c035b" sboTerm="SBO:0000290">
<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="#a42aa37c-029d-4ba1-a1d9-9dd45dfebec4">
+ <rdf:Description rdf:about="#_6f33fb08-aa05-485c-88bd-9191e78c035b">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005737" />
@@ -17,10 +17,10 @@
</rdf:RDF>
</annotation>
</compartment>
- <compartment constant="true" id="extracellular_region" metaid="e0cf247c-556c-4a08-98a4-4265ee04b383" sboTerm="SBO:0000290">
+ <compartment constant="true" id="extracellular_region" metaid="_5a314950-04a3-419e-b331-6e865f6e07ab" sboTerm="SBO:0000290">
<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="#e0cf247c-556c-4a08-98a4-4265ee04b383">
+ <rdf:Description rdf:about="#_5a314950-04a3-419e-b331-6e865f6e07ab">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005576" />
@@ -30,10 +30,10 @@
</rdf:RDF>
</annotation>
</compartment>
- <compartment constant="true" id="nucleus" metaid="c838e868-1a7a-4ead-b359-4f7510d16cd8" sboTerm="SBO:0000290">
+ <compartment constant="true" id="nucleus" metaid="_0cf11842-46ef-481b-b4fb-985008badff3" sboTerm="SBO:0000290">
<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="#c838e868-1a7a-4ead-b359-4f7510d16cd8">
+ <rdf:Description rdf:about="#_0cf11842-46ef-481b-b4fb-985008badff3">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005634" />
@@ -99,146 +99,116 @@
sboTerm="SBO:0000252" />
</listOfSpecies>
<listOfReactions>
- <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108288" name="http://pid.nci.nih.gov/biopaxpid_108288" reversible="true" sboTerm="SBO:0000177">
+ <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108288" name="http://pid.nci.nih.gov/biopaxpid_108288" reversible="false" sboTerm="SBO:0000177">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108292" name="http://pid.nci.nih.gov/biopaxpid_108292" species="http___pid_nci_nih_gov_biopaxpid_981"
- stoichiometry="1" />
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108293" name="http://pid.nci.nih.gov/biopaxpid_108293" species="http___pid_nci_nih_gov_biopaxpid_1359"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108292" species="http___pid_nci_nih_gov_biopaxpid_981" stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108293" species="http___pid_nci_nih_gov_biopaxpid_1359" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108294" name="http://pid.nci.nih.gov/biopaxpid_108294" species="http___pid_nci_nih_gov_biopaxpid_108289"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108294" species="http___pid_nci_nih_gov_biopaxpid_108289" stoichiometry="1" />
</listOfProducts>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108267" name="http://pid.nci.nih.gov/biopaxpid_108267" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108267" name="http://pid.nci.nih.gov/biopaxpid_108267" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108268" name="http://pid.nci.nih.gov/biopaxpid_108268" species="http___pid_nci_nih_gov_biopaxpid_1359"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108268" species="http___pid_nci_nih_gov_biopaxpid_1359" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108269" name="http://pid.nci.nih.gov/biopaxpid_108269" species="http___pid_nci_nih_gov_biopaxpid_1033"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108269" species="http___pid_nci_nih_gov_biopaxpid_1033" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108270" name="http://pid.nci.nih.gov/biopaxpid_108270" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_105130" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108270" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_105130" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108283" name="http://pid.nci.nih.gov/biopaxpid_108283" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108283" name="http://pid.nci.nih.gov/biopaxpid_108283" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108284" name="http://pid.nci.nih.gov/biopaxpid_108284" species="http___pid_nci_nih_gov_biopaxpid_1585"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108284" species="http___pid_nci_nih_gov_biopaxpid_1585" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108285" name="http://pid.nci.nih.gov/biopaxpid_108285" species="http___pid_nci_nih_gov_biopaxpid_1594"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108285" species="http___pid_nci_nih_gov_biopaxpid_1594" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108286" name="http://pid.nci.nih.gov/biopaxpid_108286" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_54617" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108286" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_54617" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1546" name="http://pid.nci.nih.gov/biopaxpid_1546" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1546" name="http://pid.nci.nih.gov/biopaxpid_1546" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1547" name="http://pid.nci.nih.gov/biopaxpid_1547" species="http___pid_nci_nih_gov_biopaxpid_1033"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1547" species="http___pid_nci_nih_gov_biopaxpid_1033" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1548" name="http://pid.nci.nih.gov/biopaxpid_1548" species="http___pid_nci_nih_gov_biopaxpid_1359"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1548" species="http___pid_nci_nih_gov_biopaxpid_1359" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_1549" name="http://pid.nci.nih.gov/biopaxpid_1549" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1550" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_1549" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1550" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108239" name="http://pid.nci.nih.gov/biopaxpid_108239" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108239" name="http://pid.nci.nih.gov/biopaxpid_108239" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108242" name="http://pid.nci.nih.gov/biopaxpid_108242" species="http___pid_nci_nih_gov_biopaxpid_28772"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108242" species="http___pid_nci_nih_gov_biopaxpid_28772" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108243" name="http://pid.nci.nih.gov/biopaxpid_108243" species="http___pid_nci_nih_gov_biopaxpid_108240"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108243" species="http___pid_nci_nih_gov_biopaxpid_108240" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108244" name="http://pid.nci.nih.gov/biopaxpid_108244" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_1359" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108244" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1359" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108277" name="http://pid.nci.nih.gov/biopaxpid_108277" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108277" name="http://pid.nci.nih.gov/biopaxpid_108277" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108280" name="http://pid.nci.nih.gov/biopaxpid_108280" species="http___pid_nci_nih_gov_biopaxpid_31559"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108280" species="http___pid_nci_nih_gov_biopaxpid_31559" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108281" name="http://pid.nci.nih.gov/biopaxpid_108281" species="http___pid_nci_nih_gov_biopaxpid_108278"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108281" species="http___pid_nci_nih_gov_biopaxpid_108278" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108282" name="http://pid.nci.nih.gov/biopaxpid_108282" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_1359" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108282" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1359" />
</listOfModifiers>
</reaction>
- <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108299" name="http://pid.nci.nih.gov/biopaxpid_108299" reversible="true" sboTerm="SBO:0000177">
+ <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108299" name="http://pid.nci.nih.gov/biopaxpid_108299" reversible="false" sboTerm="SBO:0000177">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108300" name="http://pid.nci.nih.gov/biopaxpid_108300" species="http___pid_nci_nih_gov_biopaxpid_6986"
- stoichiometry="1" />
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108301" name="http://pid.nci.nih.gov/biopaxpid_108301" species="http___pid_nci_nih_gov_biopaxpid_108256"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108300" species="http___pid_nci_nih_gov_biopaxpid_6986" stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108301" species="http___pid_nci_nih_gov_biopaxpid_108256" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108302" name="http://pid.nci.nih.gov/biopaxpid_108302" species="http___pid_nci_nih_gov_biopaxpid_108263"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108302" species="http___pid_nci_nih_gov_biopaxpid_108263" stoichiometry="1" />
</listOfProducts>
</reaction>
- <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108235" name="http://pid.nci.nih.gov/biopaxpid_108235" reversible="true" sboTerm="SBO:0000177">
+ <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108235" name="http://pid.nci.nih.gov/biopaxpid_108235" reversible="false" sboTerm="SBO:0000177">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108237" name="http://pid.nci.nih.gov/biopaxpid_108237" species="http___pid_nci_nih_gov_biopaxpid_48168"
- stoichiometry="1" />
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108236" name="http://pid.nci.nih.gov/biopaxpid_108236" species="http___pid_nci_nih_gov_biopaxpid_48171"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108237" species="http___pid_nci_nih_gov_biopaxpid_48168" stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108236" species="http___pid_nci_nih_gov_biopaxpid_48171" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108238" name="http://pid.nci.nih.gov/biopaxpid_108238" species="http___pid_nci_nih_gov_biopaxpid_54617"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108238" species="http___pid_nci_nih_gov_biopaxpid_54617" stoichiometry="1" />
</listOfProducts>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108295" name="http://pid.nci.nih.gov/biopaxpid_108295" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108295" name="http://pid.nci.nih.gov/biopaxpid_108295" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108296" name="http://pid.nci.nih.gov/biopaxpid_108296" species="http___pid_nci_nih_gov_biopaxpid_1352"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108296" species="http___pid_nci_nih_gov_biopaxpid_1352" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108297" name="http://pid.nci.nih.gov/biopaxpid_108297" species="http___pid_nci_nih_gov_biopaxpid_29575"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108297" species="http___pid_nci_nih_gov_biopaxpid_29575" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108298" name="http://pid.nci.nih.gov/biopaxpid_108298" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_1359" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108298" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1359" />
</listOfModifiers>
</reaction>
- <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108274" name="http://pid.nci.nih.gov/biopaxpid_108274" reversible="true" sboTerm="SBO:0000185">
+ <reaction fast="true" id="http___pid_nci_nih_gov_biopaxpid_108274" name="http://pid.nci.nih.gov/biopaxpid_108274" reversible="false" sboTerm="SBO:0000185">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108275" name="http://pid.nci.nih.gov/biopaxpid_108275" species="http___pid_nci_nih_gov_biopaxpid_108248"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108275" species="http___pid_nci_nih_gov_biopaxpid_108248" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108276" name="http://pid.nci.nih.gov/biopaxpid_108276" species="http___pid_nci_nih_gov_biopaxpid_108273"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108276" species="http___pid_nci_nih_gov_biopaxpid_108273" stoichiometry="1" />
</listOfProducts>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1615" name="http://pid.nci.nih.gov/biopaxpid_1615" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1615" name="http://pid.nci.nih.gov/biopaxpid_1615" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1618" name="http://pid.nci.nih.gov/biopaxpid_1618" species="http___pid_nci_nih_gov_biopaxpid_1616"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1618" species="http___pid_nci_nih_gov_biopaxpid_1616" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1619" name="http://pid.nci.nih.gov/biopaxpid_1619" species="http___pid_nci_nih_gov_biopaxpid_1582"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1619" species="http___pid_nci_nih_gov_biopaxpid_1582" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_1620" name="http://pid.nci.nih.gov/biopaxpid_1620" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1594" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_1620" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1594" />
</listOfModifiers>
</reaction>
<reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108271" name="http://pid.nci.nih.gov/biopaxpid_108271" reversible="false" sboTerm="SBO:0000589">
@@ -246,43 +216,37 @@
<speciesReference constant="true" species="http___pid_nci_nih_gov_biopaxpid_16844" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108272" name="http://pid.nci.nih.gov/biopaxpid_108272" sboTerm="SBO:0000021"
- species="http___pid_nci_nih_gov_biopaxpid_108273" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108272" sboTerm="SBO:0000459" species="http___pid_nci_nih_gov_biopaxpid_108273" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1577" name="http://pid.nci.nih.gov/biopaxpid_1577" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_1577" name="http://pid.nci.nih.gov/biopaxpid_1577" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1579" name="http://pid.nci.nih.gov/biopaxpid_1579" species="http___pid_nci_nih_gov_biopaxpid_1578"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1579" species="http___pid_nci_nih_gov_biopaxpid_1578" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_1580" name="http://pid.nci.nih.gov/biopaxpid_1580" species="http___pid_nci_nih_gov_biopaxpid_1550"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_1580" species="http___pid_nci_nih_gov_biopaxpid_1550" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_1581" name="http://pid.nci.nih.gov/biopaxpid_1581" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1582" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_1581" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1582" />
</listOfModifiers>
</reaction>
- <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108247" name="http://pid.nci.nih.gov/biopaxpid_108247" reversible="true" sboTerm="SBO:0000176">
+ <reaction fast="false" id="http___pid_nci_nih_gov_biopaxpid_108247" name="http://pid.nci.nih.gov/biopaxpid_108247" reversible="false" sboTerm="SBO:0000176">
<listOfReactants>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108258" name="http://pid.nci.nih.gov/biopaxpid_108258" species="http___pid_nci_nih_gov_biopaxpid_108248"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108258" species="http___pid_nci_nih_gov_biopaxpid_108248" stoichiometry="1" />
</listOfReactants>
<listOfProducts>
- <speciesReference constant="true" id="http___pid_nci_nih_gov_biopaxpid_108259" name="http://pid.nci.nih.gov/biopaxpid_108259" species="http___pid_nci_nih_gov_biopaxpid_108256"
- stoichiometry="1" />
+ <speciesReference constant="true" name="http://pid.nci.nih.gov/biopaxpid_108259" species="http___pid_nci_nih_gov_biopaxpid_108256" stoichiometry="1" />
</listOfProducts>
<listOfModifiers>
- <modifierSpeciesReference id="http___pid_nci_nih_gov_biopaxpid_108260" name="http://pid.nci.nih.gov/biopaxpid_108260" sboTerm="SBO:0000013"
- species="http___pid_nci_nih_gov_biopaxpid_1359" />
+ <modifierSpeciesReference name="http://pid.nci.nih.gov/biopaxpid_108260" sboTerm="SBO:0000013" species="http___pid_nci_nih_gov_biopaxpid_1359" />
</listOfModifiers>
</reaction>
</listOfReactions>
</comp:modelDefinition>
- <comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_15760" metaid="_5527692c-9a95-43dd-b1fa-41fd057152e3" name="apoptosis">
+ <comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_15760" metaid="f9e78160-bce9-4d4d-a6a0-b9251492cac6" name="apoptosis">
<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="#_5527692c-9a95-43dd-b1fa-41fd057152e3">
+ <rdf:Description rdf:about="#f9e78160-bce9-4d4d-a6a0-b9251492cac6">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006915" />
@@ -304,10 +268,10 @@
<comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_10409" name="cell survival">
<listOfCompartments>
<compartment constant="true" id="defaultCompartment" sboTerm="SBO:0000290" />
- <compartment constant="true" id="nucleus" metaid="cd34212a-6028-4492-82e3-d4226a147012" sboTerm="SBO:0000290">
+ <compartment constant="true" id="nucleus" metaid="_89dff4c8-7d7f-42cb-8806-b215d4402394" sboTerm="SBO:0000290">
<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="#cd34212a-6028-4492-82e3-d4226a147012">
+ <rdf:Description rdf:about="#_89dff4c8-7d7f-42cb-8806-b215d4402394">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005634" />
@@ -329,10 +293,10 @@
sboTerm="SBO:0000252" />
</listOfSpecies>
</comp:modelDefinition>
- <comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_1543" metaid="_827f3f3e-8b71-426b-9236-5b05187a05a6" name="protein ubiquitination">
+ <comp:modelDefinition id="http___pid_nci_nih_gov_biopaxpid_1543" metaid="_8ba97f4a-61ed-483d-8dd6-4f76347e30e6" name="protein ubiquitination">
<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="#_827f3f3e-8b71-426b-9236-5b05187a05a6">
+ <rdf:Description rdf:about="#_8ba97f4a-61ed-483d-8dd6-4f76347e30e6">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/go/GO:0016567" />
@@ -350,7 +314,7 @@
</listOfSpecies>
</comp:modelDefinition>
</comp:listOfModelDefinitions>
- <model id="topLevel_sbmlModel" metaid="e5cee301-b3d1-4a94-9b54-abcf48aae997">
+ <model id="topLevel_sbmlModel" metaid="_597b7403-f113-4470-b380-48ab240af5b4">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>This model has been automatically generated by BioPAX2SBML</p>
@@ -358,7 +322,7 @@
</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="#e5cee301-b3d1-4a94-9b54-abcf48aae997">
+ <rdf:Description rdf:about="#_597b7403-f113-4470-b380-48ab240af5b4">
<dc:creator>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
@@ -378,7 +342,14 @@
<comp:submodel comp:id="submodel__http___pid_nci_nih_gov_biopaxpid_1543" comp:modelRef="http___pid_nci_nih_gov_biopaxpid_1543" />
</comp:listOfSubmodels>
<listOfCompartments>
- <compartment constant="true" id="defaultCompartment" sboTerm="SBO:0000290" />
+ <compartment constant="true" id="defaultCompartment" sboTerm="SBO:0000290">
+ <comp:listOfReplacedElements xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <comp:replacedElement comp:idRef="defaultCompartment" comp:submodelRef="submodel__http___pid_nci_nih_gov_biopaxpid_108233" />
+ <comp:replacedElement comp...
[truncated message content] |
