Merge pull request #719 from SynBioHub/sbol3data

moved edited sbol3 data to tests folder
SynBioHub · Aug 28, 2024 · da6f1e9 · da6f1e9
2 parents a078b54 + d5518ff
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diff --git a/tests/SBOL3 data/New_activity.rdf b/tests/SBOL3 data/New_activity.rdf
@@ -0,0 +1,89 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/toggle_switch">
+      <sbol:description>Toggle Switch genetic circuit</sbol:description>
+      <sbol:name>Toggle Switch</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000241"/>
+      <sbol:displayId>toggle_switch</sbol:displayId>
+   </sbol:Component>
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/toggle_switch_optimised">
+      <prov:wasDerivedFrom rdf:resource="https://sbolstandard.org/examples/toggle_switch"/>
+      <prov:wasGeneratedBy rdf:resource="https://sbolstandard.org/examples/codon_optimization_activity"/>
+      <sbol:description>Toggle Switch genetic circuit - codon optimised</sbol:description>
+      <sbol:name>Toggle Switch Optimised</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000241"/>
+      <sbol:displayId>toggle_switch_optimised</sbol:displayId>
+   </sbol:Component>
+   <sbol:TopLevel rdf:about="https://sbolstandard.org/examples/CodonOptimiserSoftware">
+      <sbol:description>Used to optimise bacterial DNA sequences.</sbol:description>
+      <sbol:name>Codon Optimiser Software</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>CodonOptimiserSoftware</sbol:displayId>
+      <rdf:type rdf:resource="http://www.w3.org/ns/prov#Agent"/>
+   </sbol:TopLevel>
+   <sbol:TopLevel rdf:about="https://sbolstandard.org/examples/RBS_optimisation_activity">
+      <prov:wasInformedBy>
+         <sbol:TopLevel rdf:about="https://sbolstandard.org/examples/codon_optimization_activity"/>
+      </prov:wasInformedBy>
+      <sbol:description>An activity that is used to RBSs</sbol:description>
+      <sbol:name>RBS optimization activity</sbol:name>
+      <sbol:type rdf:resource="http://sbols.org/v3#design"/>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>RBS_optimisation_activity</sbol:displayId>
+      <rdf:type rdf:resource="http://www.w3.org/ns/prov#Activity"/>
+   </sbol:TopLevel>
+   <sbol:TopLevel rdf:about="CodonOptimisationProtocol">
+      <sbol:description>Optimisation protocol to improve the translation of mRNAs.</sbol:description>
+      <sbol:name>Codon Optimisation Protocol</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>CodonOptimisationProtocol</sbol:displayId>
+      <rdf:type rdf:resource="http://www.w3.org/ns/prov#Plan"/>
+   </sbol:TopLevel>
+   <sbol:TopLevel rdf:about="https://sbolstandard.org/examples/codon_optimization_activity">
+      <sbol:type rdf:resource="http://sbols.org/v3#design"/>
+      <prov:startedAtTime>2019-07-29T15:42:23.277Z</prov:startedAtTime>
+      <prov:endedAtTime>2020-08-30T15:42:23.277Z</prov:endedAtTime>
+      <sbol:name>Codon optimization activity</sbol:name>
+      <sbol:description>An activity that is used to optimise codons</sbol:description>
+      <prov:qualifiedUsage>
+         <sbol:Identified rdf:about="https://sbolstandard.org/examples/codon_optimization_activity/Usage2">
+            <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000011"/>
+            <prov:entity rdf:resource="https://sbolstandard.org/examples/toggle_switch_optimised"/>
+            <sbol:displayId>Usage2</sbol:displayId>
+            <rdf:type rdf:resource="http://www.w3.org/ns/prov#Usage"/>
+         </sbol:Identified>
+      </prov:qualifiedUsage>
+      <rdf:type rdf:resource="http://www.w3.org/ns/prov#Activity"/>
+      <sbol:displayId>codon_optimization_activity</sbol:displayId>
+      <prov:qualifiedAssociation>
+         <sbol:Identified rdf:about="https://sbolstandard.org/examples/codon_optimization_activity/Association1">
+            <prov:hadRole rdf:resource="http://sbols.org/v3#design"/>
+            <prov:hadPlan rdf:resource="https://sbolstandard.org/examples/CodonOptimisationProtocol"/>
+            <prov:agent rdf:resource="https://sbolstandard.org/examples/CodonOptimiserSoftware"/>
+            <sbol:displayId>Association1</sbol:displayId>
+            <rdf:type rdf:resource="http://www.w3.org/ns/prov#Association"/>
+         </sbol:Identified>
+      </prov:qualifiedAssociation>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <prov:qualifiedUsage>
+         <sbol:Identified rdf:about="https://sbolstandard.org/examples/codon_optimization_activity/Usage1">
+            <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000645"/>
+            <prov:entity rdf:resource="https://sbolstandard.org/examples/toggle_switch"/>
+            <sbol:displayId>Usage1</sbol:displayId>
+            <rdf:type rdf:resource="http://www.w3.org/ns/prov#Usage"/>
+         </sbol:Identified>
+      </prov:qualifiedUsage>
+   </sbol:TopLevel>
+</rdf:RDF>
diff --git a/tests/SBOL3 data/New_agent.rdf b/tests/SBOL3 data/New_agent.rdf
@@ -0,0 +1,27 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/toggle_switch">
+      <sbol:description>Toggle Switch genetic circuit</sbol:description>
+      <sbol:name>Toggle Switch</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000241"/>
+      <sbol:displayId>toggle_switch</sbol:displayId>
+   </sbol:Component>
+   <sbol:TopLevel rdf:about="https://sbolstandard.org/examples/CodonOptimiserSoftware">
+      <sbol:description>Used to optimise bacterial DNA sequences.</sbol:description>
+      <sbol:name>Codon Optimiser Software</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>CodonOptimiserSoftware</sbol:displayId>
+      <rdf:type rdf:resource="http://www.w3.org/ns/prov#Agent"/>
+   </sbol:TopLevel>
+</rdf:RDF>
diff --git a/tests/SBOL3 data/New_annotation.rdf b/tests/SBOL3 data/New_annotation.rdf
@@ -0,0 +1,75 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:igem="http://parts.igem.org/"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/BBa_J23119">
+      <igem:belongsTo>
+         <igem:Repository rdf:about="https://sbolstandard.org/examples/iGEMRepository">
+            <igem:website rdf:resource="http://parts.igem.org/Main_Page"/>
+            <sbol:description>Registry of Standard Biological Parts</sbol:description>
+            <sbol:name>iGEM Registry</sbol:name>
+            <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+            <sbol:displayId>iGEMRepository</sbol:displayId>
+            <rdf:type rdf:resource="http://sbols.org/v3#TopLevel"/>
+         </igem:Repository>
+      </igem:belongsTo>
+      <sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
+      <sbol:description>Parts J23100 through J23119 are a family of constitutive promoter parts isolated from a small combinatorial library.</sbol:description>
+      <igem:hasInformation>
+         <igem:Information rdf:about="https://sbolstandard.org/examples/BBa_J23119/information1">
+            <igem:regulation>//regulation/second_regulation</igem:regulation>
+            <igem:regulation>//regulation/constitutive</igem:regulation>
+            <igem:sigmaFactor>//rnap/prokaryote/ecoli/sigma70</igem:sigmaFactor>
+            <sbol:description>The experience page captures users' experience using the BBa_J23119 part</sbol:description>
+            <sbol:name>BBa_J23119_experience</sbol:name>
+            <sbol:displayId>information1</sbol:displayId>
+            <rdf:type rdf:resource="http://sbols.org/v3#Identified"/>
+         </igem:Information>
+      </igem:hasInformation>
+      <igem:belongsTo>
+         <igem:Repository rdf:about="https://sbolstandard.org/examples/SynBioHubRepository">
+            <sbol:name>SynBioHub</sbol:name>
+            <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+            <sbol:displayId>SynBioHubRepository</sbol:displayId>
+            <rdf:type rdf:resource="http://sbols.org/v3#TopLevel"/>
+         </igem:Repository>
+      </igem:belongsTo>
+      <sbol:name>BBa_J23119 part</sbol:name>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000251"/>
+      <igem:hasUsage>
+         <sbol:Identified rdf:about="https://sbolstandard.org/examples/BBa_J23119/usage1">
+            <sbol:displayId>usage1</sbol:displayId>
+            <igem:registryStar>1</igem:registryStar>
+            <sbol:name>BBa_J23119_usage</sbol:name>
+            <igem:uses>442</igem:uses>
+            <igem:twinURLs>
+               <igem:TwinPartUsage rdf:about="https://sbolstandard.org/examples/BBa_J23119/usage1/twinParts">
+                  <igem:twinURL rdf:resource="http://parts.igem.org/wiki/index.php?title=Part:BBa_M36800"/>
+                  <igem:twinURL rdf:resource="http://parts.igem.org/wiki/index.php?title=Part:BBa_M1638"/>
+                  <igem:twinURL rdf:resource="http://parts.igem.org/wiki/index.php?title=Part:BBa_J72073"/>
+                  <sbol:name>twin parts</sbol:name>
+                  <sbol:displayId>twinParts</sbol:displayId>
+                  <rdf:type rdf:resource="http://sbols.org/v3#Identified"/>
+               </igem:TwinPartUsage>
+            </igem:twinURLs>
+            <sbol:description>BBa_J23119 usage statistics</sbol:description>
+            <rdf:type rdf:resource="http://parts.igem.org/IGEMUsage"/>
+            <igem:twins>7</igem:twins>
+            <igem:inStock>true</igem:inStock>
+         </sbol:Identified>
+      </igem:hasUsage>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <igem:experienceURL rdf:resource="http://parts.igem.org/Part:BBa_J23119:Experience"/>
+      <sbol:displayId>BBa_J23119</sbol:displayId>
+      <igem:group>iGEM2006_Berkeley</igem:group>
+   </sbol:Component>
+</rdf:RDF>
diff --git a/tests/SBOL3 data/New_attachment.rdf b/tests/SBOL3 data/New_attachment.rdf
@@ -0,0 +1,36 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Implementation rdf:about="https://sbolstandard.org/examples/impl1">
+      <sbol:hasAttachment rdf:resource="https://sbolstandard.org/examples/attachment1"/>
+      <sbol:builtrdf rdf:resource="https://sbolstandard.org/examples/TetR_protein"/>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>impl1</sbol:displayId>
+   </sbol:Implementation>
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/TetR_protein">
+      <sbol:role rdf:resource="https://identifiers.org/GO:0003700"/>
+      <sbol:description>TetR protein</sbol:description>
+      <sbol:name>TetR</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
+      <sbol:displayId>TetR_protein</sbol:displayId>
+   </sbol:Component>
+   <sbol:Attachment rdf:about="https://sbolstandard.org/examples/attachment1">
+      <sbol:hashAlgorithm>Alg1</sbol:hashAlgorithm>
+      <sbol:hash>aaa</sbol:hash>
+      <sbol:size>1000</sbol:size>
+      <sbol:format rdf:resource="https://identifiers.org/edam:format_2585"/>
+      <sbol:source rdf:resource="https://sbolstandard.org/examples//attachment1"/>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>attachment1</sbol:displayId>
+   </sbol:Attachment>
+</rdf:RDF>
diff --git a/tests/SBOL3 data/New_collection.rdf b/tests/SBOL3 data/New_collection.rdf
@@ -0,0 +1,35 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Collection rdf:about="https://sbolstandard.org/examples/col1">
+      <sbol:member rdf:resource="https://sbolstandard.org/examples/LacI_protein"/>
+      <sbol:member rdf:resource="https://sbolstandard.org/examples/TetR_protein"/>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:displayId>col1</sbol:displayId>
+   </sbol:Collection>
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/LacI_protein">
+      <sbol:role rdf:resource="https://identifiers.org/GO:0003700"/>
+      <sbol:description>LacI protein</sbol:description>
+      <sbol:name>LacI</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
+      <sbol:displayId>LacI_protein</sbol:displayId>
+   </sbol:Component>
+   <sbol:Component rdf:about="https://sbolstandard.org/examples/TetR_protein">
+      <sbol:role rdf:resource="https://identifiers.org/GO:0003700"/>
+      <sbol:description>TetR protein</sbol:description>
+      <sbol:name>TetR</sbol:name>
+      <sbol:hasNamespace rdf:resource="https://sbolstandard.org/examples"/>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
+      <sbol:displayId>TetR_protein</sbol:displayId>
+   </sbol:Component>
+</rdf:RDF>