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uk.ac.ncl.intbio.examples.DataTreeCreator Maven / Gradle / Ivy
package uk.ac.ncl.intbio.examples;
import java.net.URI;
import javax.xml.namespace.QName;
import uk.ac.ncl.intbio.core.datatree.DocumentRoot;
import uk.ac.ncl.intbio.core.datatree.NamespaceBinding;
import uk.ac.ncl.intbio.core.datatree.NestedDocument;
import uk.ac.ncl.intbio.core.datatree.TopLevelDocument;
import uk.ac.ncl.intbio.core.io.rdf.RdfTerms;
import uk.ac.ncl.intbio.core.schema.SchemaCatalog;
import static uk.ac.ncl.intbio.core.datatree.Datatree.*;
import static uk.ac.ncl.intbio.core.schema.Schema.*;
/**
* Provides methods to create example Datatrees.
* @author goksel
*
*/
public class DataTreeCreator {
private static final NamespaceBinding partsRegistry = NamespaceBinding("http://partsregistry.org/", "pr");
private static final NamespaceBinding sbolExample = NamespaceBinding("http://sbolstandard.org/example#", "example");
private static final NamespaceBinding obo = NamespaceBinding("http://purl.obolibrary.org/obo/", "obo");
private static final NamespaceBinding utah = NamespaceBinding("http://www.async.ece.utah.edu/", "utah");
// private static String dctermsNS = "http://purl.org/dc/terms/";
// private static String dctermsPF = "dcterms";
/**
* Creates an example {@link DocumentRoot} object with data from the SBOL2.0 proposed data model.
* Included SBOL objects are Module, Interaction, Participation, ComponentInstantiation and Model.
* @return {@link DocumentRoot}
*/
public static DocumentRoot makeSBOL2Document()
{
NestedDocument instantiationLacI=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/LacI_instantiation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "LacI")
));
NestedDocument instantiationIPTG=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/IPTG"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "IPTG")
));
NestedDocument instantiationIPTGLacI=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/IPTG_LacI_complex"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "IPTG LacI complex")
));
NestedDocument instantiationpLac=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/pLac_instantiation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "pLac promoter")
));
NestedDocument instantiationcTetR=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/cTetR_instantiation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "cTetR")
));
NestedDocument instantiationTetR=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("module_LacI_inverter/TetR_instantiation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "TetR")
));
NestedDocument interactionIPTGBinding=NestedDocument(
Sbol2Terms.module.interaction,
sbolExample.namespacedUri("module_LacI_inverter/interaction/IPTG_binding"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "IPTG Binding"),
NamedProperty(RdfTerms.rdfType, URI.create("http://purl.obolibrary.org/obo/non_covalent_binding")),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/IPTG_Binding/LacI_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role,URI.create("http://purl.obolibrary.org/obo/reactant")),
NamedProperty(Sbol2Terms.module.participant, instantiationLacI.getIdentity())
)
)
),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/IPTG_Binding/IPTGLacI_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role, URI.create("http://purl.obolibrary.org/obo/product")),
NamedProperty(Sbol2Terms.module.participant, instantiationIPTGLacI.getIdentity())
)
)),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/IPTG_Binding/IPTG_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role, URI.create("http://purl.obolibrary.org/obo/reactant")),
NamedProperty(Sbol2Terms.module.participant, instantiationIPTG.getIdentity())
)
)
)
)
);
NestedDocument interactionLacIRepression=NestedDocument(
Sbol2Terms.module.interaction,
sbolExample.namespacedUri("module_LacI_inverter/interaction/LacI_repression"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "LacI Repression"),
NamedProperty(RdfTerms.rdfType, URI.create("http://purl.obolibrary.org/obo/repression")),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/LacI_repression/LacI"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role,URI.create("http://purl.obolibrary.org/obo/repressor")),
NamedProperty(Sbol2Terms.module.participant, instantiationLacI.getIdentity())
)
)
),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/LacI_repression/pLac"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role, URI.create("http://purl.obolibrary.org/obo/repressed")),
NamedProperty(Sbol2Terms.module.participant, instantiationpLac.getIdentity())
)
)
)
)
);
NestedDocument interactionTetRTranscriptionTranslation=NestedDocument(
Sbol2Terms.module.interaction,
sbolExample.namespacedUri("module_LacI_inverter/interaction/TetR_transcription_translation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "TetR Transcription Translation"),
NamedProperty(RdfTerms.rdfType, URI.create("http://purl.obolibrary.org/obo/genetic_production")),
NamedProperty(RdfTerms.rdfType, URI.create("http://made.up.terms.org/unicorns")),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/TetR_transcription_translation/TetR_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role,URI.create("http://purl.obolibrary.org/obo/product")),
NamedProperty(Sbol2Terms.module.participant, instantiationTetR.getIdentity())
)
)
),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/TetR_transcription_translation/cTetR_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role, URI.create("http://purl.obolibrary.org/obo/transcribed")),
NamedProperty(Sbol2Terms.module.participant, instantiationcTetR.getIdentity())
)
)
),
NamedProperty(Sbol2Terms.module.hasParticipation,
NestedDocument(
Sbol2Terms.module.participation,
partsRegistry.namespacedUri("module_LacI_inverter/interaction/TetR_transcription_translation/pLac_participation"),
NamedProperties(
NamedProperty(Sbol2Terms.module.role, URI.create("http://purl.obolibrary.org/obo/modifier")),
NamedProperty(Sbol2Terms.module.participant, instantiationpLac.getIdentity())
)
)
)
)
);
TopLevelDocument modelLacIInverter=TopLevelDocument(
NamespaceBindings(utah),
Sbol2Terms.model.model,
sbolExample.namespacedUri("model/LacI_inverter"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "LacI Inverter Model"),
NamedProperty(Sbol2Terms.model.source,URI.create("http://www.async.ece.utah.edu/LacI_Inverter.xml")),
NamedProperty(Sbol2Terms.model.language,"SBML"),
NamedProperty(Sbol2Terms.model.framework,"ODE"),
NamedProperty(Sbol2Terms.model.role,"simulation")
)
);
TopLevelDocument moduleLacIInverter=TopLevelDocument(
Sbol2Terms.module.module,
sbolExample.namespacedUri("module/LacI_inverter"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "LacI Inverter"),
NamedProperty(Sbol2Terms.module.hasInteraction, interactionIPTGBinding),
NamedProperty(Sbol2Terms.module.hasInteraction, interactionLacIRepression),
NamedProperty(Sbol2Terms.module.hasInteraction, interactionTetRTranscriptionTranslation),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationLacI),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationIPTG),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationIPTGLacI),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationpLac),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationcTetR),
NamedProperty(Sbol2Terms.instantiation.hasComponentInstantiation, instantiationTetR),
NamedProperty(Sbol2Terms.module.hasModel,modelLacIInverter.getIdentity())
)
);
return DocumentRoot(
NamespaceBindings(RdfTerms.rdf, SbolTerms.sbol2, partsRegistry, sbolExample, obo),
TopLevelDocuments(moduleLacIInverter,modelLacIInverter));
}
/**
* Creates an example {@link DocumentRoot} object with data from the SBOL2.0 proposed data model.
* Included SBOL objects from the data model are SequenceComponent, ComponentInstantiation, SequenceAnnotation and SequenceComponent.
* @return {@link DocumentRoot}
*/
public static DocumentRoot makeSBOL2SequenceComponent()
{
TopLevelDocument pLac=TopLevelDocument(
Sbol2Terms.component.sequenceComponent,
sbolExample.namespacedUri("sequenceComponent/pLac"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "pLac"),
NamedProperty(Sbol2Terms.documented.displayId, "pLac"),
NamedProperty(RdfTerms.rdfType, URI.create("DNA")),
NamedProperty(Sbol2Terms.component.sequenceType, URI.create("http://purl.org/obo/owl/SO#SO_0000167"))
));
NestedDocument instantiationpLac=NestedDocument(
Sbol2Terms.instantiation.componentInstantiation,
sbolExample.namespacedUri("sequenceComponent/pLac/instantiation"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "pLac"),
NamedProperty(Sbol2Terms.component.component, pLac.getIdentity())
));
NestedDocument pLacAnnotation=NestedDocument(
Sbol2Terms.component.sequenceAnnotation,
sbolExample.namespacedUri("sequenceComponent/UU_002/pLac_annotation"),
NamedProperties(
NamedProperty(Sbol2Terms.component.orientation, "inline"),
NamedProperty(Sbol2Terms.instantiation.subComponentInstantiation, instantiationpLac)
));
TopLevelDocument lacIRepressibleGeneSequence=TopLevelDocument(
Sbol2Terms.component.sequence,
sbolExample.namespacedUri("sequenceComponent/UU_002/sequence"),
NamedProperties(
NamedProperty(Sbol2Terms.component.elements, "atg")
));
TopLevelDocument lacIRepressibleGene=TopLevelDocument(
Sbol2Terms.component.sequenceComponent,
sbolExample.namespacedUri("sequenceComponent/UU_002"),
NamedProperties(
NamedProperty(Sbol2Terms.documented.name, "LacI Repressible Gene"),
NamedProperty(Sbol2Terms.documented.displayId, "UU_002"),
NamedProperty(RdfTerms.rdfType, URI.create("DNA")),
NamedProperty(Sbol2Terms.component.sequenceType, URI.create("http://purl.org/obo/owl/SO#SO_0000774")),
NamedProperty(Sbol2Terms.component.annotation, pLacAnnotation),
NamedProperty(Sbol2Terms.component.hasSequence, lacIRepressibleGeneSequence.getIdentity())
));
return DocumentRoot(
NamespaceBindings(SbolTerms.sbol2),
TopLevelDocuments(lacIRepressibleGene,pLac,lacIRepressibleGeneSequence)
);
}
/**
* Creates an example {@link DocumentRoot} object with data from the SBOL1.1 data model.
* Included SBOL objects are DnaComponent, SequenceAnnotation and DnaSequence.
* @return {@link DocumentRoot}
*/
public static DocumentRoot makeDocument()
{
return DocumentRoot(
NamespaceBindings(SbolTerms.sbol2),
TopLevelDocuments(
TopLevelDocument(
SbolTerms.dnaComponent,
partsRegistry.namespacedUri("Part:BBa_I0462"),
NamedProperties(
NamedProperty(SbolTerms.name, "I0462"),
NamedProperty(SbolTerms.description, "LuxR protein generator"),
NamedProperty(SbolTerms.dnaSequence, partsRegistry.namespacedUri("Part:BBa_I0462/sequence")),
NamedProperty(
SbolTerms.sequenceAnnotation,
NestedDocument(
SbolTerms.annotation,
partsRegistry.namespacedUri("Part:BBa_I0462/anot/1234567"),
NamedProperties(
NamedProperty(SbolTerms.bioStart, 1),
NamedProperty(SbolTerms.bioEnd, 12),
NamedProperty(SbolTerms.strand, "+"),
NamedProperty(
SbolTerms.subComponent,
partsRegistry.namespacedUri("Part:BBa_B0034")
)
)
)
),
NamedProperty(
SbolTerms.annotation,
NestedDocument(
SbolTerms.sequenceAnnotation,
partsRegistry.namespacedUri("Part:BBa_I0462/annotation/2345678"),
NamedProperties(
NamedProperty(SbolTerms.bioStart, 19),
NamedProperty(SbolTerms.bioEnd, 774),
NamedProperty(SbolTerms.subComponent, partsRegistry.namespacedUri("Part:BBa_C0062"))
)
)
)
)
),
TopLevelDocument(
SbolTerms.dnaSequence,
partsRegistry.namespacedUri("Part:BBa_I0462/sequence"),
NamedProperties(NamedProperty(
SbolTerms.nucleotides,
"aaagaggagaaatactagatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcactactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata"
))
),
TopLevelDocument(
SbolTerms.dnaComponent,
partsRegistry.namespacedUri("Part:BBa_B0034"),
NamedProperties(
NamedProperty(SbolTerms.name, "I0462"),
NamedProperty(SbolTerms.displayId, "BBa_B0034"),
NamedProperty(RdfTerms.rdfType, URI.create("http://purl.obolibrary.org/obo/SO_0000139"))
)),
TopLevelDocument(
SbolTerms.dnaComponent,
partsRegistry.namespacedUri("Part:BBa_C0062"),
NamedProperties(
NamedProperty(SbolTerms.name, "luxR"),
NamedProperty(SbolTerms.displayId, "BBa_C0062"),
NamedProperty(RdfTerms.rdfType, URI.create("http://purl.obolibrary.org/obo/SO_0000316"))
)
)
));
}
/**
* Creates a {@link SchemaCatalog} for the SBOL20 core objects
* @return {@link SchemaCatalog}
*/
public static SchemaCatalog makeCoreSchemaCatalog()
{
return SchemaCatalog(
Sbol2Terms.sbol2.namespacedUri("/schemaexample/core"),
ImportedSchemas(),
DocumentSchemas(
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/identified"),
Extends(),
IdentifierSchemas(),
TypeSchemas(),
PropertySchemas()
),
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/documented"),
Extends(Sbol2Terms.sbol2.namespacedUri("/schema/identified")),
IdentifierSchemas(),
TypeSchemas(),
PropertySchemas(
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.documented.displayId)
),
cardinality.required,
PropertyValueSchemas(propertyType.string)
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.documented.name)
),
cardinality.optional,
PropertyValueSchemas(propertyType.string)
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.documented.description)
),
cardinality.optional,
PropertyValueSchemas(propertyType.string)
)
)
)
)
);
}
/**
* Creates a {@link SchemaCatalog} for the SBOL20 instantiation objects
* @return {@link SchemaCatalog}
*/
public static SchemaCatalog makeInstantiationSchemaCatalog()
{
return SchemaCatalog(
Sbol2Terms.sbol2.namespacedUri("/schemaexample/instantiation"),
ImportedSchemas(),
DocumentSchemas(
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/component_instantiation"),
Extends(),
IdentifierSchemas(),
TypeSchemas(
TypeSchema(Sbol2Terms.instantiation.componentInstantiation)
),
PropertySchemas(
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.instantiation.hasComponentInstantiation)
),
cardinality.required,
PropertyValueSchemas(ReferenceValue(Sbol2Terms.sbol2.namespacedUri("/schema/sequence_component")))
)
)
)
)
);
}
/**
* Creates a {@link SchemaCatalog} for the SBOL20 component objects
* @return {@link SchemaCatalog}
*/
public static SchemaCatalog makeComponentSchemaCatalog()
{
return SchemaCatalog(
Sbol2Terms.sbol2.namespacedUri("/schemaexample/component"),
ImportedSchemas(
Sbol2Terms.sbol2.namespacedUri("/schema/core"),
Sbol2Terms.sbol2.namespacedUri("/schema/instantiation")
),
DocumentSchemas(
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/sequence"),
Extends(),
IdentifierSchemas(),
TypeSchemas(
TypeSchema(Sbol2Terms.component.sequence)
),
PropertySchemas(
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.elements)
),
cardinality.required,
PropertyValueSchemas(propertyType.string)
)
)
),
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/sequence_component"),
Extends(Sbol2Terms.sbol2.namespacedUri("/schema/documented")),
IdentifierSchemas(),
TypeSchemas(
TypeSchema(Sbol2Terms.component.sequenceComponent)
),
PropertySchemas(
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.hasSequence)
),
cardinality.optional,
PropertyValueSchemas(ReferenceValue(Sbol2Terms.sbol2.namespacedUri("/schema/sequence")))
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.annotation)
),
cardinality.many,
PropertyValueSchemas(
DocumentValue(
DocumentSchema(
Sbol2Terms.sbol2.namespacedUri("/schema/sequence_annotation"),
Extends(Sbol2Terms.sbol2.namespacedUri("/schema/documented")),
IdentifierSchemas(),
TypeSchemas(
TypeSchema(Sbol2Terms.component.sequenceComponent)
),
PropertySchemas(
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.instantiation.subComponentInstantiation)
),
cardinality.required,
PropertyValueSchemas(ReferenceValue(Sbol2Terms.sbol2.namespacedUri("/schema/component_instantiation")))
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.orientation)
),
cardinality.required,
PropertyValueSchemas(propertyType.oneOf("inline","reverse_compliment"))
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.start)
),
cardinality.optional,
PropertyValueSchemas(propertyType.integer)
),
PropertySchema(
TypeSchemas(
TypeSchema(Sbol2Terms.component.end)
),
cardinality.optional,
PropertyValueSchemas(propertyType.integer)
)
)
)
)
)
)
)
)
)
);
}
}
