Add SBOL types to the PROV classes

All non-SBOL types that make use of properties in the SBOL namespace
should have two RDF types, one outside the SBOL namespace and one
inside the SBOL namespace. The provenance examples only had the RDF
type that was outside the SBOL namespace, while using properties
within the SBOL namespace like http://sbols.org/v3#displayId and
http://sbols.org/v3#name.

Author: tcmitchell

SBOL3/provenance_entity/activity/activity.nt

@@ -1,49 +1,57 @@
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasDerivedFrom> <https://sbolstandard.org/examples/toggle_switch> .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://sbolstandard.org/examples/codon_optimization_activity> .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#description> "Toggle Switch genetic circuit - codon optimised" .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#displayId> "toggle_switch_optimised" .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000241> .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#name> "Toggle Switch Optimised" .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
+
+<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#description> "Optimisation protocol to improve the translation of mRNAs." .
+<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#displayId> "CodonOptimisationProtocol" .
+<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#name> "Codon Optimisation Protocol" .
+<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
+<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Plan> .
 <https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://sbols.org/v3#description> "Used to optimise bacterial DNA sequences." .
-<https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://sbols.org/v3#name> "Codon Optimiser Software" .
 <https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://sbols.org/v3#displayId> "CodonOptimiserSoftware" .
+<https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://sbols.org/v3#name> "Codon Optimiser Software" .
+<https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
 <https://sbolstandard.org/examples/CodonOptimiserSoftware> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> .
-<https://sbolstandard.org/examples/RBS_optimisation_activity> <http://www.w3.org/ns/prov#wasInformedBy> <https://sbolstandard.org/examples/codon_optimization_activity> .
 <https://sbolstandard.org/examples/RBS_optimisation_activity> <http://sbols.org/v3#description> "An activity that is used to RBSs" .
+<https://sbolstandard.org/examples/RBS_optimisation_activity> <http://sbols.org/v3#displayId> "RBS_optimisation_activity" .
 <https://sbolstandard.org/examples/RBS_optimisation_activity> <http://sbols.org/v3#name> "RBS optimization activity" .
 <https://sbolstandard.org/examples/RBS_optimisation_activity> <http://sbols.org/v3#type> <http://sbols.org/v3#design> .
-<https://sbolstandard.org/examples/RBS_optimisation_activity> <http://sbols.org/v3#displayId> "RBS_optimisation_activity" .
+<https://sbolstandard.org/examples/RBS_optimisation_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
 <https://sbolstandard.org/examples/RBS_optimisation_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
-<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/ns/prov#hadRole> <https://identifiers.org/SBO:0000645> .
-<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/ns/prov#entity> <https://sbolstandard.org/examples/toggle_switch> .
-<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://sbols.org/v3#displayId> "source_usage" .
-<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Usage> .
-<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/ns/prov#hadRole> <https://identifiers.org/SBO:0000011> .
-<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/ns/prov#entity> <https://sbolstandard.org/examples/toggle_switch_optimised> .
-<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://sbols.org/v3#displayId> "optimised_usage" .
-<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Usage> .
-<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#description> "Toggle Switch genetic circuit" .
-<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#displayId> "toggle_switch" .
-<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000241> .
-<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#name> "Toggle Switch" .
-<https://sbolstandard.org/examples/toggle_switch> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
-<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadRole> <http://sbols.org/v3#design> .
-<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadPlan> <https://sbolstandard.org/examples/CodonOptimisationProtocol> .
-<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadAgent> <https://sbolstandard.org/examples/CodonOptimiserSoftware> .
+<https://sbolstandard.org/examples/RBS_optimisation_activity> <http://www.w3.org/ns/prov#wasInformedBy> <https://sbolstandard.org/examples/codon_optimization_activity> .
 <https://sbolstandard.org/examples/codon_optimization_activity/association> <http://sbols.org/v3#displayId> "association" .
+<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
 <https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Association> .
-<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#description> "Optimisation protocol to improve the translation of mRNAs." .
-<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#name> "Codon Optimisation Protocol" .
-<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://sbols.org/v3#displayId> "CodonOptimisationProtocol" .
-<https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Plan> .
+<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadAgent> <https://sbolstandard.org/examples/CodonOptimiserSoftware> .
+<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadPlan> <https://sbolstandard.org/examples/CodonOptimisationProtocol> .
+<https://sbolstandard.org/examples/codon_optimization_activity/association> <http://www.w3.org/ns/prov#hadRole> <http://sbols.org/v3#design> .
+<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://sbols.org/v3#displayId> "optimised_usage" .
+<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Usage> .
+<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/ns/prov#entity> <https://sbolstandard.org/examples/toggle_switch_optimised> .
+<https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> <http://www.w3.org/ns/prov#hadRole> <https://identifiers.org/SBO:0000011> .
+<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://sbols.org/v3#displayId> "source_usage" .
+<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Identified> .
+<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Usage> .
+<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/ns/prov#entity> <https://sbolstandard.org/examples/toggle_switch> .
+<https://sbolstandard.org/examples/codon_optimization_activity/source_usage> <http://www.w3.org/ns/prov#hadRole> <https://identifiers.org/SBO:0000645> .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#description> "An activity that is used to optimise codons" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#displayId> "codon_optimization_activity" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#name> "Codon optimization activity" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#type> <http://sbols.org/v3#design> .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T22:25:17.44Z" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedAssociation> <https://sbolstandard.org/examples/codon_optimization_activity/association> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#name> "Codon optimization activity" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T22:25:17.44Z" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#description> "An activity that is used to optimise codons" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T22:25:17.44Z" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#displayId> "codon_optimization_activity" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/source_usage> .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T22:25:17.44Z" .
+<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#description> "Toggle Switch genetic circuit" .
+<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#displayId> "toggle_switch" .
+<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#name> "Toggle Switch" .
+<https://sbolstandard.org/examples/toggle_switch> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000241> .
+<https://sbolstandard.org/examples/toggle_switch> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#description> "Toggle Switch genetic circuit - codon optimised" .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#displayId> "toggle_switch_optimised" .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#name> "Toggle Switch Optimised" .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000241> .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasDerivedFrom> <https://sbolstandard.org/examples/toggle_switch> .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://sbolstandard.org/examples/codon_optimization_activity> .