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SynBioDex / libSBOLj

Java Library for Synthetic Biology Open Language (SBOL)
Apache License 2.0
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Add RDF triple store read support #168

Closed ckmadsen closed 8 years ago

ckmadsen commented 9 years ago

When attempting to parse the following RDF file, we get the following error:

access is not an SBOL object, so it cannot be in the SBOL namespace.

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:sbolhub="http://sbolhub.org/"
    xmlns:sbol="http://sbols.org/v2#"
    xmlns:sbol1="http://sbols.org/v1#"
    xmlns:prov="http://www.w3.org/ns/prov#" > 
  <rdf:Description rdf:about="http://www.partsregistry.org/ECK120033736">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/ECK120033736"/>
    <dcterms:description>Terminator2</dcterms:description>
    <dcterms:title>ECK120033736</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
    <sbol:displayId>ECK120033736</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/ECK120033736"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
    <sbol:displayId>BBa_R0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno3">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040"/>
    <sbol:displayId>anno3</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno3"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1"/>
    <sbol:displayId>pIKELeftCassette_1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/tetr_inverter">
    <sbol:mapsTo rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping"/>
    <sbol:definition rdf:resource="http://sbolstandard.org/example/tetr_inverter"/>
    <sbol:displayId>tetr_inverter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Module"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>55</sbol:end>
    <sbol:start>1</sbol:start>
    <sbol:displayId>location1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_R0040">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_R0040"/>
    <dcterms:description>pTet promoter</dcterms:description>
    <dcterms:title>pTetR</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
    <sbol:displayId>BBa_R0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>55</sbol:end>
    <sbol:start>1</sbol:start>
    <sbol:displayId>location1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch">
    <sbol:module rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter"/>
    <sbol:module rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter"/>
    <sbol:model rdf:resource="http://sbolstandard.org/example/toogleswicth"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/toggle_switch/LacI"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/toggle_switch/TetR"/>
    <sbol:role rdf:resource="http://sbolstandard.org/example/module_role/toggle_switch"/>
    <sbol:displayId>toggle_switch</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ModuleDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010">
    <sbol:participant rdf:resource="http://sbolstandard.org/example/laci_inverter/promoter"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000598"/>
    <sbol:displayId>BBa_R0010</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Participation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI">
    <sbol:participation rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040"/>
    <sbol:participation rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72"/>
    <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000169"/>
    <sbol:displayId>LacI_pLacI</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Interaction"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>1288</sbol:end>
    <sbol:start>1198</sbol:start>
    <sbol:displayId>location4</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_C0012">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa</sbol:elements>
    <sbol:displayId>BBa_C0012</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_C0012"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://identifiers.org/uniprot/P42212">
    <dcterms:description>GFP protein</dcterms:description>
    <dcterms:title>GFP</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000011"/>
    <sbol:displayId>P42212</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/P42212"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter">
    <sbol:interaction rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/tetr_inverter/promoter"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
    <sbol:role rdf:resource="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter"/>
    <sbol:displayId>tetr_inverter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ModuleDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno4">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130"/>
    <sbol:displayId>anno4</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno4"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1">
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2"/>
    <dcterms:title>LacI/TetR Toggle Switch</dcterms:title>
    <dcterms:description>LacI/TetR Toggle Switch</dcterms:description>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
    <sbol:displayId>pIKE_Toggle_1</sbol:displayId>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1"/>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040"/>
    <sbol:displayId>anno1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>2834</sbol:end>
    <sbol:start>1286</sbol:start>
    <sbol:displayId>location2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_C0040">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_C0040"/>
    <dcterms:description>tetR coding sequence</dcterms:description>
    <dcterms:title>tetR</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
    <sbol:displayId>BBa_C0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_C0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_R0040">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac</sbol:elements>
    <sbol:displayId>BBa_R0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_R0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping">
    <sbol:local rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
    <sbol:remote rdf:resource="http://sbolstandard.org/example/toggle_switch/TetR"/>
    <sbol:refinement rdf:resource="http://sbols.org/v2#useRemote"/>
    <sbol:displayId>TetR_mapping</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping"/>
    <rdf:type rdf:resource="http://sbols.org/v2#MapsTo"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023">
    <sbol:participant rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
    <sbol:displayId>P03023</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Participation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_J61120">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>aaagacaggacc</sbol:elements>
    <sbol:displayId>BBa_J61120</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_J61120"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>1197</sbol:end>
    <sbol:start>69</sbol:start>
    <sbol:displayId>location3</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolhub.org/gen/spam_sbolhub_220715163411_sbol2_220715174456">
    <sbolhub:purpose>spam3</sbolhub:purpose>
    <sbolhub:name>spam3</sbolhub:name>
    <sbolhub:description>spam3</sbolhub:description>
    <sbolhub:keywords></sbolhub:keywords>
    <sbolhub:intended_chassis></sbolhub:intended_chassis>
    <sbol:displayId>spam_sbolhub_220715163411_sbol2_220715174456</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolhub.org/gen/spam_sbolhub_220715163411_sbol2_220715174456"/>
    <rdf:type rdf:resource="http://sbolhub.org/UploadData"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_J61120"/>
    <sbol:displayId>BBa_J61120</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>729</sbol:end>
    <sbol:start>69</sbol:start>
    <sbol:displayId>location3</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>1554</sbol:end>
    <sbol:start>1464</sbol:start>
    <sbol:displayId>location6</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolhub.org/col/spam_sbolhub_220715163411_sbol2_220715174456">
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_J61101"/>
    <sbol:persistentIdentity rdf:resource="http://sbolhub.org/col/spam_sbolhub_220715163411_sbol2_220715174456"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_C0040"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1"/>
    <sbol:member rdf:resource="http://sbolstandard.org/example/tetr_inverter"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_R0040"/>
    <sbol:displayId>spam_sbolhub_220715163411_sbol2_220715174456</sbol:displayId>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_J61130"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_E0040"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_R0010"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/ECK120033736"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/ECK120029600"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/ECK120033736"/>
    <sbol:member rdf:resource="http://sbolstandard.org/example/laci_inverter"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_J61130"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Collection"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/ECK120029600"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_J61101"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_C0012"/>
    <dcterms:creator>sbolhub</dcterms:creator>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_J61120"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_J61120"/>
    <sbol:member rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
    <sbol:member rdf:resource="http://identifiers.org/uniprot/P42212"/>
    <sbol:member rdf:resource="http://www.virtualparts.org/part/BBa_C0012"/>
    <sbol:member rdf:resource="http://sbolstandard.org/example/toggle_switch"/>
    <sbol:member rdf:resource="http://sbolhub.org/gen/spam_sbolhub_220715163411_sbol2_220715174456"/>
    <sbol:member rdf:resource="http://identifiers.org/uniprot/P03023"/>
    <sbol:member rdf:resource="http://sbolstandard.org/example/toogleswicth"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_E0040"/>
    <sbol:member rdf:resource="http://www.partsregistry.org/BBa_C0040"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
    <sbol:displayId>BBa_R0010</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_E0040"/>
    <sbol:displayId>BBa_E0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/ECK120029600">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</sbol:elements>
    <sbol:displayId>ECK120029600</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/ECK120029600"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_J61101"/>
    <sbol:displayId>BBa_J61101</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_J61120">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61120"/>
    <dcterms:description>RBS2</dcterms:description>
    <dcterms:title>BBa_J61101 RBS</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
    <sbol:displayId>BBa_J61120</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61120"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://identifiers.org/uniprot/P03023">
    <dcterms:description>LacI protein</dcterms:description>
    <dcterms:title>LacI</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
    <sbol:displayId>P03023</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/P03023"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno1">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010"/>
    <sbol:displayId>anno1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter/TF">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
    <sbol:displayId>TF</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno5">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040"/>
    <sbol:displayId>anno5</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno5"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>68</sbol:end>
    <sbol:start>56</sbol:start>
    <sbol:displayId>location2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_C0012"/>
    <sbol:displayId>BBa_C0012</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101"/>
    <sbol:displayId>anno2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/TetR">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
    <sbol:displayId>TetR</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/TetR"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1">
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno5"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno6"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno2"/>
    <dcterms:description>LacI Inverter</dcterms:description>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno4"/>
    <dcterms:title>LacI Inverter</dcterms:title>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno1"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno3"/>
    <sbol:displayId>pIKERightCassette_1</sbol:displayId>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72">
    <sbol:participant rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
    <sbol:displayId>Q6QR72</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Participation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/ECK120033736">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</sbol:elements>
    <sbol:displayId>ECK120033736</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/ECK120033736"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/LacI">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://identifiers.org/uniprot/P03023"/>
    <sbol:displayId>LacI</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/LacI"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_E0040">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_E0040"/>
    <dcterms:description>gfp coding sequence</dcterms:description>
    <dcterms:title>gfp</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
    <sbol:displayId>BBa_E0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_E0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_C0040"/>
    <sbol:displayId>BBa_C0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040">
    <sbol:participant rdf:resource="http://sbolstandard.org/example/tetr_inverter/promoter"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000598"/>
    <sbol:displayId>BBa_R0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Participation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_J61101">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>aaagacaggacc</sbol:elements>
    <sbol:displayId>BBa_J61101</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_J61101"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1"/>
    <sbol:displayId>anno2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/laci_inverter">
    <sbol:mapsTo rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping"/>
    <sbol:definition rdf:resource="http://sbolstandard.org/example/laci_inverter"/>
    <sbol:displayId>laci_inverter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Module"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_R0010">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_R0010"/>
    <dcterms:description>pLacI promoter</dcterms:description>
    <dcterms:title>pLacI</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
    <sbol:displayId>BBa_R0010</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI">
    <sbol:participation rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010"/>
    <sbol:participation rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023"/>
    <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000169"/>
    <sbol:displayId>LacI_pLacI</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Interaction"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_C0012">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_C0012"/>
    <dcterms:description>lacI coding sequence</dcterms:description>
    <dcterms:title>lacI</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
    <sbol:displayId>BBa_C0012</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_C0012"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012"/>
    <sbol:displayId>anno3</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter/promoter">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
    <sbol:displayId>promoter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/promoter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter">
    <sbol:interaction rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
    <sbol:functionalComponent rdf:resource="http://sbolstandard.org/example/laci_inverter/promoter"/>
    <sbol:role rdf:resource="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter"/>
    <sbol:displayId>laci_inverter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ModuleDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_J61101">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61101"/>
    <dcterms:description>RBS1</dcterms:description>
    <dcterms:title>BBa_J61101 RBS</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
    <sbol:displayId>BBa_J61101</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61101"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1">
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1"/>
    <dcterms:description>TetR Inverter</dcterms:description>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600"/>
    <sbol:displayId>pIKELeftCassette_1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1"/>
    <sbol:sequenceAnnotation rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2"/>
    <dcterms:title>TetR Inverter</dcterms:title>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>68</sbol:end>
    <sbol:start>56</sbol:start>
    <sbol:displayId>location2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/ECK120029600"/>
    <sbol:displayId>ECK120029600</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_C0040">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa</sbol:elements>
    <sbol:displayId>BBa_C0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_C0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno2">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120"/>
    <sbol:displayId>anno2</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno2"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>1463</sbol:end>
    <sbol:start>743</sbol:start>
    <sbol:displayId>location5</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>742</sbol:end>
    <sbol:start>730</sbol:start>
    <sbol:displayId>location4</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1"/>
    <sbol:displayId>pIKERightCassette_1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_E0040">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa</sbol:elements>
    <sbol:displayId>BBa_E0040</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_E0040"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toogleswicth">
    <sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
    <sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
    <sbol:source rdf:resource="http://virtualparts.org/part/pIKE_Toggle_1"/>
    <sbol:displayId>toogleswicth</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toogleswicth"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Model"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/ECK120033736"/>
    <sbol:displayId>ECK120033736</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_R0010">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac</sbol:elements>
    <sbol:displayId>BBa_R0010</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_R0010"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1"/>
    <sbol:displayId>anno1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/ECK120029600">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/ECK120029600"/>
    <dcterms:description>Terminator1</dcterms:description>
    <dcterms:title>ECK120029600</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
    <sbol:displayId>ECK120029600</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/ECK120029600"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130">
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_J61130"/>
    <sbol:displayId>BBa_J61130</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Component"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://identifiers.org/uniprot/Q6QR72">
    <dcterms:description>TetR protein</dcterms:description>
    <dcterms:title>TetR</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
    <sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
    <sbol:displayId>Q6QR72</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping">
    <sbol:local rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
    <sbol:remote rdf:resource="http://sbolstandard.org/example/toggle_switch/LacI"/>
    <sbol:refinement rdf:resource="http://sbols.org/v2#useRemote"/>
    <sbol:displayId>LacI_mapping</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping"/>
    <rdf:type rdf:resource="http://sbols.org/v2#MapsTo"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600"/>
    <sbol:displayId>anno4</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.partsregistry.org/BBa_J61130">
    <sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61130"/>
    <dcterms:description>RBS2</dcterms:description>
    <dcterms:title>BBa_J61101 RBS</dcterms:title>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
    <sbol:displayId>BBa_J61130</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61130"/>
    <rdf:type rdf:resource="http://sbols.org/v2#ComponentDefinition"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/anno6">
    <sbol:location rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6"/>
    <sbol:component rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736"/>
    <sbol:displayId>anno6</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/anno6"/>
    <rdf:type rdf:resource="http://sbols.org/v2#SequenceAnnotation"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1">
    <sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
    <sbol:end>1285</sbol:end>
    <sbol:start>1</sbol:start>
    <sbol:displayId>location1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Range"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/laci_inverter/TF">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://identifiers.org/uniprot/P03023"/>
    <sbol:displayId>TF</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://sbolstandard.org/example/tetr_inverter/promoter">
    <sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
    <sbol:access rdf:resource="http://sbols.org/v2#public"/>
    <sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
    <sbol:displayId>promoter</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/promoter"/>
    <rdf:type rdf:resource="http://sbols.org/v2#FunctionalComponent"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.virtualparts.org/part/BBa_J61130">
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
    <sbol:elements>aaagaaacgaca</sbol:elements>
    <sbol:displayId>BBa_J61130</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/BBa_J61130"/>
    <rdf:type rdf:resource="http://sbols.org/v2#Sequence"/>
  </rdf:Description>
</rdf:RDF>
cjmyers commented 9 years ago

Hi Curtis,

This is not a valid SBOL2 file. Please have a look at the example files in the specification. SBOL is not generic flat RDF triples. It is nested RDF/XML in a particular form. Each top level object must come at the top level and be tagged properly. Each child object (like a sequence annotation) must come nested within a top level object. You will need to format this file properly to get it to parse in.

Chris

On Jul 22, 2015, at 11:04 AM, Curtis Madsen notifications@github.com wrote:

When attempting to parse the following RDF file, we get the following error:

access is not an SBOL object, so it cannot be in the SBOL namespace.

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:sbolhub="http://sbolhub.org/" xmlns:sbol="http://sbols.org/v2#" xmlns:sbol1="http://sbols.org/v1#" xmlns:prov="http://www.w3.org/ns/prov#" >

dcterms:descriptionTerminator2/dcterms:description dcterms:titleECK120033736/dcterms:title sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:displayIdanno3/sbol:displayId /rdf:Description sbol:displayIdpIKELeftCassette_1/sbol:displayId /rdf:Description sbol:displayIdtetr_inverter/sbol:displayId /rdf:Description sbol:end55/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description dcterms:descriptionpTet promoter/dcterms:description dcterms:titlepTetR/dcterms:title sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:end55/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description sbol:displayIdtoggle_switch/sbol:displayId /rdf:Description sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdLacI_pLacI/sbol:displayId /rdf:Description sbol:end1288/sbol:end sbol:start1198/sbol:start sbol:displayIdlocation4/sbol:displayId /rdf:Description sbol:elementsatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtct cactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa/sbol:elements sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description dcterms:descriptionGFP protein/dcterms:description dcterms:titleGFP/dcterms:title sbol:displayIdP42212/sbol:displayId /rdf:Description sbol:displayIdtetr_inverter/sbol:displayId /rdf:Description sbol:displayIdanno4/sbol:displayId /rdf:Description dcterms:titleLacI/TetR Toggle Switch/dcterms:title dcterms:descriptionLacI/TetR Toggle Switch/dcterms:description sbol:displayIdpIKE_Toggle_1/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description sbol:end2834/sbol:end sbol:start1286/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description dcterms:descriptiontetR coding sequence/dcterms:description dcterms:titletetR/dcterms:title sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:elementstccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac/sbol:elements sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:displayIdTetR_mapping/sbol:displayId /rdf:Description sbol:displayIdP03023/sbol:displayId /rdf:Description sbol:elementsaaagacaggacc/sbol:elements sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description sbol:end1197/sbol:end sbol:start69/sbol:start sbol:displayIdlocation3/sbol:displayId /rdf:Description sbolhub:purposespam3/sbolhub:purpose sbolhub:namespam3/sbolhub:name sbolhub:descriptionspam3/sbolhub:description sbolhub:keywords/sbolhub:keywords sbolhub:intended_chassis/sbolhub:intended_chassis sbol:displayIdspam_sbolhub_220715163411_sbol2_220715174456/sbol:displayId /rdf:Description sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description sbol:end729/sbol:end sbol:start69/sbol:start sbol:displayIdlocation3/sbol:displayId /rdf:Description sbol:end1554/sbol:end sbol:start1464/sbol:start sbol:displayIdlocation6/sbol:displayId /rdf:Description sbol:displayIdspam_sbolhub_220715163411_sbol2_220715174456/sbol:displayId dcterms:creatorsbolhub/dcterms:creator /rdf:Description sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:elementsttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa/sbol:elements sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description dcterms:descriptionRBS2/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description dcterms:descriptionLacI protein/dcterms:description dcterms:titleLacI/dcterms:title sbol:displayIdP03023/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description sbol:displayIdTF/sbol:displayId /rdf:Description sbol:displayIdanno5/sbol:displayId /rdf:Description sbol:end68/sbol:end sbol:start56/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:displayIdTetR/sbol:displayId /rdf:Description dcterms:descriptionLacI Inverter/dcterms:description dcterms:titleLacI Inverter/dcterms:title sbol:displayIdpIKERightCassette_1/sbol:displayId /rdf:Description sbol:displayIdQ6QR72/sbol:displayId /rdf:Description sbol:elementsttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa/sbol:elements sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:displayIdLacI/sbol:displayId /rdf:Description dcterms:descriptiongfp coding sequence/dcterms:description dcterms:titlegfp/dcterms:title sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:elementsaaagacaggacc/sbol:elements sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:displayIdlaci_inverter/sbol:displayId /rdf:Description dcterms:descriptionpLacI promoter/dcterms:description dcterms:titlepLacI/dcterms:title sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdLacI_pLacI/sbol:displayId /rdf:Description dcterms:descriptionlacI coding sequence/dcterms:description dcterms:titlelacI/dcterms:title sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description sbol:displayIdanno3/sbol:displayId /rdf:Description sbol:displayIdpromoter/sbol:displayId /rdf:Description sbol:displayIdlaci_inverter/sbol:displayId /rdf:Description dcterms:descriptionRBS1/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description dcterms:descriptionTetR Inverter/dcterms:description sbol:displayIdpIKELeftCassette_1/sbol:displayId dcterms:titleTetR Inverter/dcterms:title /rdf:Description sbol:end68/sbol:end sbol:start56/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:elementsatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa/sbol:elements sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:end1463/sbol:end sbol:start743/sbol:start sbol:displayIdlocation5/sbol:displayId /rdf:Description sbol:end742/sbol:end sbol:start730/sbol:start sbol:displayIdlocation4/sbol:displayId /rdf:Description sbol:displayIdpIKERightCassette_1/sbol:displayId /rdf:Description sbol:elementsatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa/sbol:elements sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:displayIdtoogleswicth/sbol:displayId /rdf:Description sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:elementstccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac/sbol:elements sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description dcterms:descriptionTerminator1/dcterms:description dcterms:titleECK120029600/dcterms:title sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description dcterms:descriptionTetR protein/dcterms:description dcterms:titleTetR/dcterms:title sbol:displayIdQ6QR72/sbol:displayId /rdf:Description sbol:displayIdLacI_mapping/sbol:displayId /rdf:Description sbol:displayIdanno4/sbol:displayId /rdf:Description dcterms:descriptionRBS2/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description sbol:displayIdanno6/sbol:displayId /rdf:Description sbol:end1285/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description sbol:displayIdTF/sbol:displayId /rdf:Description sbol:displayIdpromoter/sbol:displayId /rdf:Description sbol:elementsaaagaaacgaca/sbol:elements sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description /rdf:RDF — Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/168.
cjmyers commented 9 years ago

One more thing. The reason you get this error message is it is parsing all “Description” objects as generic top level entities. Access is not a valid field for a generic top level which is why you get this error. I suppose the error message could be improved.

Chris

On Jul 22, 2015, at 11:04 AM, Curtis Madsen notifications@github.com wrote:

When attempting to parse the following RDF file, we get the following error:

access is not an SBOL object, so it cannot be in the SBOL namespace.

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:sbolhub="http://sbolhub.org/" xmlns:sbol="http://sbols.org/v2#" xmlns:sbol1="http://sbols.org/v1#" xmlns:prov="http://www.w3.org/ns/prov#" >

dcterms:descriptionTerminator2/dcterms:description dcterms:titleECK120033736/dcterms:title sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:displayIdanno3/sbol:displayId /rdf:Description sbol:displayIdpIKELeftCassette_1/sbol:displayId /rdf:Description sbol:displayIdtetr_inverter/sbol:displayId /rdf:Description sbol:end55/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description dcterms:descriptionpTet promoter/dcterms:description dcterms:titlepTetR/dcterms:title sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:end55/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description sbol:displayIdtoggle_switch/sbol:displayId /rdf:Description sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdLacI_pLacI/sbol:displayId /rdf:Description sbol:end1288/sbol:end sbol:start1198/sbol:start sbol:displayIdlocation4/sbol:displayId /rdf:Description sbol:elementsatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtct cactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa/sbol:elements sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description dcterms:descriptionGFP protein/dcterms:description dcterms:titleGFP/dcterms:title sbol:displayIdP42212/sbol:displayId /rdf:Description sbol:displayIdtetr_inverter/sbol:displayId /rdf:Description sbol:displayIdanno4/sbol:displayId /rdf:Description dcterms:titleLacI/TetR Toggle Switch/dcterms:title dcterms:descriptionLacI/TetR Toggle Switch/dcterms:description sbol:displayIdpIKE_Toggle_1/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description sbol:end2834/sbol:end sbol:start1286/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description dcterms:descriptiontetR coding sequence/dcterms:description dcterms:titletetR/dcterms:title sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:elementstccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac/sbol:elements sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:displayIdTetR_mapping/sbol:displayId /rdf:Description sbol:displayIdP03023/sbol:displayId /rdf:Description sbol:elementsaaagacaggacc/sbol:elements sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description sbol:end1197/sbol:end sbol:start69/sbol:start sbol:displayIdlocation3/sbol:displayId /rdf:Description sbolhub:purposespam3/sbolhub:purpose sbolhub:namespam3/sbolhub:name sbolhub:descriptionspam3/sbolhub:description sbolhub:keywords/sbolhub:keywords sbolhub:intended_chassis/sbolhub:intended_chassis sbol:displayIdspam_sbolhub_220715163411_sbol2_220715174456/sbol:displayId /rdf:Description sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description sbol:end729/sbol:end sbol:start69/sbol:start sbol:displayIdlocation3/sbol:displayId /rdf:Description sbol:end1554/sbol:end sbol:start1464/sbol:start sbol:displayIdlocation6/sbol:displayId /rdf:Description sbol:displayIdspam_sbolhub_220715163411_sbol2_220715174456/sbol:displayId dcterms:creatorsbolhub/dcterms:creator /rdf:Description sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:elementsttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa/sbol:elements sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description dcterms:descriptionRBS2/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61120/sbol:displayId /rdf:Description dcterms:descriptionLacI protein/dcterms:description dcterms:titleLacI/dcterms:title sbol:displayIdP03023/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description sbol:displayIdTF/sbol:displayId /rdf:Description sbol:displayIdanno5/sbol:displayId /rdf:Description sbol:end68/sbol:end sbol:start56/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:displayIdTetR/sbol:displayId /rdf:Description dcterms:descriptionLacI Inverter/dcterms:description dcterms:titleLacI Inverter/dcterms:title sbol:displayIdpIKERightCassette_1/sbol:displayId /rdf:Description sbol:displayIdQ6QR72/sbol:displayId /rdf:Description sbol:elementsttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa/sbol:elements sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:displayIdLacI/sbol:displayId /rdf:Description dcterms:descriptiongfp coding sequence/dcterms:description dcterms:titlegfp/dcterms:title sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:displayIdBBa_R0040/sbol:displayId /rdf:Description sbol:elementsaaagacaggacc/sbol:elements sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:displayIdlaci_inverter/sbol:displayId /rdf:Description dcterms:descriptionpLacI promoter/dcterms:description dcterms:titlepLacI/dcterms:title sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdLacI_pLacI/sbol:displayId /rdf:Description dcterms:descriptionlacI coding sequence/dcterms:description dcterms:titlelacI/dcterms:title sbol:displayIdBBa_C0012/sbol:displayId /rdf:Description sbol:displayIdanno3/sbol:displayId /rdf:Description sbol:displayIdpromoter/sbol:displayId /rdf:Description sbol:displayIdlaci_inverter/sbol:displayId /rdf:Description dcterms:descriptionRBS1/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61101/sbol:displayId /rdf:Description dcterms:descriptionTetR Inverter/dcterms:description sbol:displayIdpIKELeftCassette_1/sbol:displayId dcterms:titleTetR Inverter/dcterms:title /rdf:Description sbol:end68/sbol:end sbol:start56/sbol:start sbol:displayIdlocation2/sbol:displayId /rdf:Description sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:elementsatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa/sbol:elements sbol:displayIdBBa_C0040/sbol:displayId /rdf:Description sbol:displayIdanno2/sbol:displayId /rdf:Description sbol:end1463/sbol:end sbol:start743/sbol:start sbol:displayIdlocation5/sbol:displayId /rdf:Description sbol:end742/sbol:end sbol:start730/sbol:start sbol:displayIdlocation4/sbol:displayId /rdf:Description sbol:displayIdpIKERightCassette_1/sbol:displayId /rdf:Description sbol:elementsatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa/sbol:elements sbol:displayIdBBa_E0040/sbol:displayId /rdf:Description sbol:displayIdtoogleswicth/sbol:displayId /rdf:Description sbol:displayIdECK120033736/sbol:displayId /rdf:Description sbol:elementstccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac/sbol:elements sbol:displayIdBBa_R0010/sbol:displayId /rdf:Description sbol:displayIdanno1/sbol:displayId /rdf:Description dcterms:descriptionTerminator1/dcterms:description dcterms:titleECK120029600/dcterms:title sbol:displayIdECK120029600/sbol:displayId /rdf:Description sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description dcterms:descriptionTetR protein/dcterms:description dcterms:titleTetR/dcterms:title sbol:displayIdQ6QR72/sbol:displayId /rdf:Description sbol:displayIdLacI_mapping/sbol:displayId /rdf:Description sbol:displayIdanno4/sbol:displayId /rdf:Description dcterms:descriptionRBS2/dcterms:description dcterms:titleBBa_J61101 RBS/dcterms:title sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description sbol:displayIdanno6/sbol:displayId /rdf:Description sbol:end1285/sbol:end sbol:start1/sbol:start sbol:displayIdlocation1/sbol:displayId /rdf:Description sbol:displayIdTF/sbol:displayId /rdf:Description sbol:displayIdpromoter/sbol:displayId /rdf:Description sbol:elementsaaagaaacgaca/sbol:elements sbol:displayIdBBa_J61130/sbol:displayId /rdf:Description /rdf:RDF — Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/168.
ckmadsen commented 9 years ago

So libSBOLj can't parse generic RDF files? I was hoping that I would be able to use it to convert an RDF file I pull from my triplestore repository into an SBOL Document.

Curtis

cjmyers commented 9 years ago

That is correct. It cannot parse these types of files or convert them. All of your objects are converted into GenericTopLevel which is not what you want.

Chris

On Jul 22, 2015, at 11:20 AM, Curtis Madsen notifications@github.com wrote:

So libSBOLj can't parse generic RDF files? I was hoping that I would be able to use it to convert an RDF file I pull from my triplestore repository into an SBOL Document.

Curtis

— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/168#issuecomment-123796974.

ckmadsen commented 9 years ago

Alright. Thanks for the clarification. I just thought a method called "readRDF" would be able to handle generic RDF files.

cjmyers commented 9 years ago

I can see how this might be confusing. We could perhaps change the method name to readRDFXML, if this is more clear. Note that “read” method aliases to readRDF, so perhaps this method is even unnecessary. Open to suggestions on this.

I do agree that such a helper method that converts from generic RDF to RDF/XML might be useful. Maybe Matthew/Goksel can be convinced to create such a method in their library which is what we use for parsing. However, this is technically an illegal SBOL file, so I don’t think libSBOL should natively support reading them.

I do agree also that our error message is not good, so I’ve changed it so it will be:

+ " is an illegal annotation, since annotations cannot be in the SBOL namespace." I hope this is more clear as what was happening is that it was trying to make these annotations since they were unexpected content. We cannot have though unexpected content in the sbol namespace as we would then be unable to tell users when they have typos in their tags. Cheers, Chris > On Jul 22, 2015, at 11:24 AM, Curtis Madsen notifications@github.com wrote: > > Alright. Thanks for the clarification. I just thought a method called "readRDF" would be able to handle generic RDF files. > > — > Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/168#issuecomment-123798400.
ckmadsen commented 9 years ago

I agree that the more descriptive error message is better. Thanks for updating this.

I also understand and agree that parsing generic RDF is outside the scope of libSBOLj. I was just hoping that my job was already done for me. :-)

I'll go ahead and use the document creation methods in libSBOLj to construct an SBOL document from the RDF that I get back from my triplestore.

Cheers,

Curtis

cjmyers commented 9 years ago

Reopening this one as a place holder for adding RDF triple read support to libSBOLj.

cjmyers commented 8 years ago

This complete and test cases added for it.