diff --git a/scripts/JavaFails b/scripts/JavaFails
deleted file mode 100644
index 60013e4..0000000
--- a/scripts/JavaFails
+++ /dev/null
@@ -1,48 +0,0 @@
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence1.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence2.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence3.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence4.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_ref.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleModel.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleSequence.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/test_source_location.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/toggle.xml
diff --git a/scripts/JavaNotMatch.txt b/scripts/JavaNotMatch.txt
deleted file mode 100644
index 60013e4..0000000
--- a/scripts/JavaNotMatch.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence1.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence2.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence3.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence4.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_ref.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleModel.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleSequence.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/test_source_location.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/toggle.xml
diff --git a/scripts/java23.xml b/scripts/java23.xml
deleted file mode 100644
index ebb8607..0000000
--- a/scripts/java23.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-
-
-
- ACGTURYSWKMBDHVN-.
-
- pLacSeq
-
-
diff --git a/scripts/java32.xml b/scripts/java32.xml
deleted file mode 100644
index 983009f..0000000
--- a/scripts/java32.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-
-
-
-
- ToggleModel
- 1.0
-
-
-
-
-
diff --git a/scripts/out b/scripts/out
deleted file mode 100644
index 6dc4862..0000000
--- a/scripts/out
+++ /dev/null
@@ -1,47004 +0,0 @@
-File: /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:14:56 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Activity http://sys-bio.org/Activity_build_generation/1.0.0 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 1
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml, not in python32.xml:
- http://www.partsregistry.org/act/activityId, http://sbols.org/v2#type, http://purl.obolibrary.org/obo/CHEBI_23924
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:14:59 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Activity http://www.partsregistry.org/act/activityId not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 2
-File: /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_J23119/anno/information, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://partsregistry.org/Information
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/information, http://partsregistry.org/cd/BBa_J23119/anno/information
- http://partsregistry.org/cd/BBa_J23119/anno/information, http://partsregistry.org/regulation, //regulation/constitutive
- http://partsregistry.org/cd/BBa_J23119/anno/information, http://partsregistry.org/sigmafactor, //rnap/prokaryote/ecoli/sigma70
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:01 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:02 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_J23119 differ.
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 3
-File: /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 625, in visit_document
- self.visit_attachment(obj)
- ~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 545, in visit_attachment
- raise NotImplementedError('Conversion of Attachment from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of Attachment from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml, not in python32.xml:
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Attachment
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Attachment/characterization_protocol
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#displayId, characterization_protocol
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://purl.org/dc/terms/created, 2003-12-04T12:00:00Z
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#source, file:///Users/myers/git/SBOLTestSuite/SBOL2/dynamic_measurement.mdx
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#version, 1.0.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml:
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/description, Constitutive promoter
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/experience, http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#displayId, BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/group, iGEM2006_Berkeley
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:04 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:04 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Attachment http://sys-bio.org/Attachment/characterization_protocol/1.0.0 differ.
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 4
-File: /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 625, in visit_document
- self.visit_attachment(obj)
- ~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 545, in visit_attachment
- raise NotImplementedError('Conversion of Attachment from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of Attachment from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml, not in python32.xml:
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#source, file:///Users/myers/git/SBOLTestSuite/SBOL2/dynamic_measurement.mdx
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Attachment
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#displayId, characterization_protocol
- http://sys-bio.org/Attachment/characterization_protocol/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Attachment/characterization_protocol
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml:
- http://partsregistry.org/cd/BBa_J23119, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/group, iGEM2006_Berkeley
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/description, Constitutive promoter
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/experience, http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#displayId, BBa_J23119
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:06 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:07 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Attachment http://sys-bio.org/Attachment/characterization_protocol/1.0.0 differ.
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 5
-File: /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml, not in python32.xml:
- http://www.async.ece.utah.edu/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://sbols.org/v2#elements, aaagaggagaaatactagatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcactactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://sbols.org/v2#displayId, seq_d23749adb3a7e0e2f09168cb7267a6113b238973
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation
- http://www.async.ece.utah.edu/BBa_B0015, http://purl.org/dc/terms/title, B0015
- http://www.async.ece.utah.edu/BBa_I0462, http://purl.org/dc/terms/description, LuxR protein generator
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, http://sbols.org/anot#1234567
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://sbols.org/v2#end, 774
- http://www.async.ece.utah.edu/BBa_C0062, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/BBa_B0034, http://purl.org/dc/terms/title, B0034
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://sbols.org/v2#start, 808
- http://www.async.ece.utah.edu/BBa_B0015, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_B0015
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, http://sbols.org/anot#3456789
- http://www.async.ece.utah.edu/BBa_I0462, http://purl.org/dc/terms/title, I0462
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/BBa_C0062, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034
- http://www.async.ece.utah.edu/BBa_B0015, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://sbols.org/v2#displayId, BBa_C0062_annotation
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#displayId, BBa_I0462
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, http://sbols.org/anot#2345678
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://sbols.org/v2#start, 19
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_B0015
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_B0015, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_B0034
- http://www.async.ece.utah.edu/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_B0034
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/BBa_C0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://www.w3.org/ns/prov#wasDerivedFrom, http://sbols.org/seq#d23749adb3a7e0e2f09168cb7267a6113b238973
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_B0015
- http://www.async.ece.utah.edu/BBa_B0034, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015
- http://www.async.ece.utah.edu/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range, http://sbols.org/v2#end, 12
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://www.async.ece.utah.edu/BBa_B0034, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_B0034
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation
- http://www.async.ece.utah.edu/BBa_C0062, http://purl.org/dc/terms/title, luxR
- http://www.async.ece.utah.edu/BBa_C0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range
- http://www.async.ece.utah.edu/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/BBa_B0015, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://sbols.org/v2#end, 936
- http://www.async.ece.utah.edu/BBa_B0034, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://www.async.ece.utah.edu/BBa_B0034, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/BBa_I0462, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_I0462
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation, http://sbols.org/v2#displayId, BBa_B0015_annotation
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_I0462, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#component, http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015
- http://www.async.ece.utah.edu/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_I0462, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_I0462
- http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973
- http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation, http://sbols.org/v2#displayId, BBa_B0034_annotation
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml:
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#displayId, BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/group, iGEM2006_Berkeley
- http://partsregistry.org/cd/BBa_J23119, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/experience, http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/description, Constitutive promoter
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:09 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:10 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://www.async.ece.utah.edu/BBa_I0462 differ.
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation not found in java32.xml
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation not found in java32.xml
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation not found in java32.xml
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_range not found in BBa_I0462.xml
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_range not found in BBa_I0462.xml
-->SequenceAnnotation http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_range not found in BBa_I0462.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 6
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_J23119/cutat10/cut, http://sbols.org/v2#at, 10
- http://partsregistry.org/cd/BBa_J23119/cutat12/cut, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/cutat12/cut
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119 promoter
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_J23119/cutat10
- http://partsregistry.org/cd/BBa_J23119/cutat12, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_J23119/cutat12/cut
- http://partsregistry.org/cd/BBa_J23119/cutat12/cut, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_J23119/cutat12/cut, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Cut
- http://partsregistry.org/cd/BBa_J23119/cutat12/cut, http://sbols.org/v2#displayId, cut
- http://partsregistry.org/cd/BBa_J23119/cutat10, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/cutat10
- http://partsregistry.org/cd/BBa_J23119/cutat10, http://sbols.org/v2#displayId, cutat10
- http://partsregistry.org/cd/BBa_J23119/cutat10/cut, http://sbols.org/v2#displayId, cut
- http://partsregistry.org/cd/BBa_J23119, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_J23119
- http://partsregistry.org/cd/BBa_J23119/cutat10, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_J23119/cutat10/cut
- http://partsregistry.org/cd/BBa_J23119/cutat10/cut, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/cutat10/cut
- http://partsregistry.org/cd/BBa_J23119/cutat12, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/cutat12
- http://partsregistry.org/cd/BBa_J23119/cutat10/cut, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Cut
- http://partsregistry.org/cd/BBa_J23119/cutat10/cut, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_J23119/cutat12/cut, http://sbols.org/v2#at, 12
- http://partsregistry.org/cd/BBa_J23119/cutat12, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_J23119/cutat12
- http://partsregistry.org/cd/BBa_J23119/cutat10, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_J23119/cutat12, http://sbols.org/v2#displayId, cutat12
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml:
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/group, iGEM2006_Berkeley
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/experience, http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:12 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:12 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11501 - The value of the at property of a Cut MUST be greater than or equal to zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 10,
- Property: components[0].sequenceFeatures[0].locations[0].at,
- Entity URI: http://partsregistry.org/cd/BBa_J23119/cutat10/cut,
- Entity Type: class org.sbolstandard.core3.entity.Cut
-
-sbol3-11501 - The value of the at property of a Cut MUST be greater than or equal to zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 12,
- Property: components[0].sequenceFeatures[1].locations[0].at,
- Entity URI: http://partsregistry.org/cd/BBa_J23119/cutat12/cut,
- Entity Type: class org.sbolstandard.core3.entity.Cut
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_J23119 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0062 not found in CD_SA_Cut_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_I0462 not found in CD_SA_Cut_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_B0015 not found in CD_SA_Cut_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_B0034 not found in CD_SA_Cut_Example.xml
-Sequence http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973 not found in CD_SA_Cut_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 7
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 781, in visit_sequence_annotation
- l3 = self.visit_range(l2)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 755, in visit_range
- cdef.sequence = seq_stup
- ^^^^^^^^
-NameError: name 'seq_stup' is not defined. Did you mean: 'seq_stub'?
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_J23119/rangeAt12, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3
- http://partsregistry.org/cd/BBa_J23119, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_J23119/rangeAt12
- http://partsregistry.org/cd/BBa_J23119, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/Part:BBa_J23119
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_J23119/rangeAt12, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_J23119/rangeAt12, http://sbols.org/v2#displayId, rangeAt12
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://sbols.org/v2#end, 1197
- http://partsregistry.org/cd/BBa_J23119/rangeAt12, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_J23119/rangeAt12
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://sbols.org/v2#displayId, location3
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119 promoter
- http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3, http://sbols.org/v2#start, 69
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml:
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/experience, http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119
- http://partsregistry.org/cd/BBa_J23119, http://purl.org/dc/terms/title, J23119
- http://partsregistry.org/cd/BBa_J23119, http://partsregistry.org/group, iGEM2006_Berkeley
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:14 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:15 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 69,
- Property: components[0].sequenceFeatures[0].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1197,
- Property: components[0].sequenceFeatures[0].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_J23119/rangeAt12/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_J23119 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0062 not found in CD_SA_Range_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_I0462 not found in CD_SA_Range_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_B0015 not found in CD_SA_Range_Example.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_B0034 not found in CD_SA_Range_Example.xml
-Sequence http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973 not found in CD_SA_Range_Example.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
-Python Score = 1
-Java Score = 0
-Number of Files = 8
-File: /Users/myers/git/SBOLTestSuite/SBOL2/Collection.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/Collection.xml, not in python32.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/Collection.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Collection.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:17 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:18 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/Collection.xml
-Python Score = 1
-Java Score = 1
-Number of Files = 9
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/description, luxR coding sequence
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_C0062
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/description, Double terminator
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/title, BBa_R0062
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/title, BBa_F2620
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#displayId, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/title, BBa_C0062
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/description, LuxR inducible promoter
- http://partsregistry.org/cd/BBa_F2620/rbs, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#displayId, rbs
- http://partsregistry.org/cd/BBa_F2620/ter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#displayId, gl
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#displayId, luxR
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#displayId, ter
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#displayId, GenericLocationComponent
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#displayId, pTetR
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/description, RBS based on Elowitz repressilator
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/title, BBa_B0034
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/description, 3OC6HSL -> PoPS Receiver
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#displayId, gl_seqAnn
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/title, BBa_R0040
- http://www.async.ece.utah.edu/GenericLocationComponent, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620
- http://partsregistry.org/cd/BBa_F2620, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#displayId, pLuxR
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0062
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/title, BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#displayId, anno2
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/luxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0040
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#displayId, GenericLocation
- http://partsregistry.org/cd/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/description, TetR repressible promoter
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#displayId, GenericLocation_anno2
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#displayId, myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Collection
- http://www.async.ece.utah.edu/myParts/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/myParts
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:20 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:21 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://www.async.ece.utah.edu/GenericLocationComponent differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_F2620 differ.
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno2 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/rbs_GenericLocation_anno2 not found in ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
-Python Score = 1
-Java Score = 1
-Number of Files = 10
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#displayId, luxR
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#elements, atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/title, BBa_C0062
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/description, RBS based on Elowitz repressilator
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/description, 3OC6HSL -> PoPS Receiver
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#elements, ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/description, Double terminator
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#displayId, GenericLocation
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/ter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/description, LuxR inducible promoter
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#displayId, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#displayId, ter
- http://partsregistry.org/cd/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/rbs, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/seq/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/title, BBa_B0034
- http://partsregistry.org/cd/BBa_F2620, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/luxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/seq/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/title, BBa_R0062
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_C0062
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#displayId, anno2
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/title, BBa_R0040
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#elements, acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/luxR
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://www.async.ece.utah.edu/GenericLocationComponent, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#elements, aaagaggagaaa
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#displayId, GenericLocationComponent
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/seq/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/title, BBa_B0015
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620
- http://partsregistry.org/cd/BBa_F2620/anno2/GenericLocation_anno2, http://sbols.org/v2#displayId, GenericLocation_anno2
- http://partsregistry.org/cd/BBa_F2620/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/title, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#displayId, pTetR
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/description, TetR repressible promoter
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/description, luxR coding sequence
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#displayId, rbs
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#displayId, pLuxR
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#displayId, gl
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/seq/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0040
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#displayId, gl_seqAnn
- http://partsregistry.org/seq/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/myParts/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Collection
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#displayId, myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/myParts
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:23 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:24 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:701, Calculated location length:0, Sequence: http://partsregistry.org/seq/BBa_C0062,
- Value: [http://partsregistry.org/cd/BBa_F2620/rbs/GenericLocation_anno2],
- Property: components[2].subComponents[2].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0040 differ.
-ComponentDefinition http://www.async.ece.utah.edu/GenericLocationComponent differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0062 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_B0034 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_B0015 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_F2620 differ.
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno2 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/rbs_GenericLocation_anno2 not found in ComponentDefinitionOutput_gl_noRange.xml
-ComponentDefinition http://partsregistry.org/cd/BBa_C0062 differ.
-Sequence http://partsregistry.org/seq/BBa_R0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0015 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_C0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_R0040 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0034 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
-Python Score = 1
-Java Score = 1
-Number of Files = 11
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/seq/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/title, BBa_F2620
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/description, Double terminator
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/seq/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#displayId, luxR
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://partsregistry.org/cd/BBa_F2620/anno1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno3
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#displayId, GenericLocationComponent
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno5/range
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#displayId, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#end, 956
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/title, BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#elements, atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno4
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#displayId, anno5
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#start, 1
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#displayId, pLuxR
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/description, luxR coding sequence
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#end, 770
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/description, 3OC6HSL -> PoPS Receiver
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno4/range
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#displayId, GenericLocation
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2/range
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/title, BBa_R0062
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#elements, ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/luxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#displayId, anno4
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/seq/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#elements, aaagaggagaaa
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno5
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno1/range
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#displayId, ter
- http://www.async.ece.utah.edu/GenericLocationComponent, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/description, TetR repressible promoter
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#end, 68
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#displayId, anno1
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/seq/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#end, 900
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno1
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#displayId, anno3
- http://partsregistry.org/cd/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#start, 901
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/title, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#displayId, pTetR
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno4/range
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno1/range
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_C0062
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#displayId, gl_seqAnn
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno5
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/cd/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/anno5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno5/range
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/description, LuxR inducible promoter
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#displayId, anno2
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0062
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/title, BBa_B0015
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/description, RBS based on Elowitz repressilator
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#displayId, rbs
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno2/range
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#elements, acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa
- http://www.async.ece.utah.edu/GenericLocationComponent, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericLocationComponent
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno3/range
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/gl, http://sbols.org/v2#displayId, gl
- http://partsregistry.org/cd/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/ter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/title, BBa_C0062
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#end, 55
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno4
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#start, 69
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno1
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn, http://sbols.org/v2#location, http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#start, 56
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#start, 771
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620
- http://partsregistry.org/seq/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/rbs, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno3
- http://www.async.ece.utah.edu/GenericLocationComponent/gl_seqAnn/GenericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno3/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Collection
- http://www.async.ece.utah.edu/myParts/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#displayId, myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:26 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:27 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 771,
- Property: components[2].subComponents[1].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:129, Calculated location length:130, Sequence: http://partsregistry.org/seq/BBa_B0015,
- Value: [http://partsregistry.org/cd/BBa_F2620/ter/range],
- Property: components[2].subComponents[1].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[2].subComponents[4].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 69,
- Property: components[2].subComponents[0].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 55,
- Property: components[2].subComponents[4].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 68,
- Property: components[2].subComponents[2].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 56,
- Property: components[2].subComponents[2].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 956,
- Property: components[2].subComponents[3].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 900,
- Property: components[2].subComponents[1].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:701, Calculated location length:13, Sequence: http://partsregistry.org/seq/BBa_C0062,
- Value: [http://partsregistry.org/cd/BBa_F2620/rbs/range],
- Property: components[2].subComponents[2].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:55, Calculated location length:56, Sequence: http://partsregistry.org/seq/BBa_R0062,
- Value: [http://partsregistry.org/cd/BBa_F2620/pLuxR/range],
- Property: components[2].subComponents[3].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 770,
- Property: components[2].subComponents[0].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:12, Calculated location length:702, Sequence: http://partsregistry.org/seq/BBa_B0034,
- Value: [http://partsregistry.org/cd/BBa_F2620/luxR/range],
- Property: components[2].subComponents[0].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:54, Calculated location length:55, Sequence: http://partsregistry.org/seq/BBa_R0040,
- Value: [http://partsregistry.org/cd/BBa_F2620/pTetR/range],
- Property: components[2].subComponents[4].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 901,
- Property: components[2].subComponents[3].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0040 differ.
-ComponentDefinition http://www.async.ece.utah.edu/GenericLocationComponent differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0062 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_F2620 differ.
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno5 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno4 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno3 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno1 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno2 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/rbs_GenericLocation_anno2 not found in ComponentDefinitionOutput_gl.xml
-ComponentDefinition http://partsregistry.org/cd/BBa_B0034 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_B0015 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_C0062 differ.
-Sequence http://partsregistry.org/seq/BBa_R0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0015 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_C0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_R0040 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0034 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
-Python Score = 1
-Java Score = 1
-Number of Files = 12
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 781, in visit_sequence_annotation
- l3 = self.visit_range(l2)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 755, in visit_range
- cdef.sequence = seq_stup
- ^^^^^^^^
-NameError: name 'seq_stup' is not defined. Did you mean: 'seq_stub'?
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml, not in python32.xml:
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/title, BBa_B0034
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/description, luxR coding sequence
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#displayId, pTetR
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno3
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno5
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno3/range
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/seq/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#end, 770
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno5
- http://partsregistry.org/cd/BBa_F2620/anno4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno4
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/description, Double terminator
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#displayId, anno3
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno3/range
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/luxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/description, LuxR inducible promoter
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno1
- http://partsregistry.org/seq/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://partsregistry.org/cd/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#elements, acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#displayId, anno1
- http://partsregistry.org/cd/BBa_R0062, http://purl.org/dc/terms/title, BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#displayId, anno2
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/description, TetR repressible promoter
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#start, 771
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/description, 3OC6HSL -> PoPS Receiver
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pTetR
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#end, 55
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/ter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#end, 68
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno4/range
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/seq/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno3, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno1/range
- http://partsregistry.org/cd/BBa_R0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#displayId, anno4
- http://partsregistry.org/seq/BBa_B0034, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#displayId, rbs
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno4
- http://partsregistry.org/cd/BBa_F2620/anno1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#start, 56
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_B0034, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0034
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#displayId, ter
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#elements, atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac
- http://partsregistry.org/cd/BBa_B0015, http://purl.org/dc/terms/title, BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno5/range
- http://partsregistry.org/cd/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno5/range
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620, http://purl.org/dc/terms/title, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620/anno1, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno1/range
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2/range
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_C0062
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno4/range
- http://partsregistry.org/seq/BBa_B0015, http://sbols.org/v2#elements, ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#start, 901
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno1
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0040
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#displayId, BBa_B0034
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#displayId, pLuxR
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#displayId, BBa_R0062
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_C0062
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/ter, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_B0015
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/cd/BBa_B0015, http://sbols.org/v2#displayId, BBa_B0015
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/pLuxR
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/luxR, http://sbols.org/v2#displayId, luxR
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#displayId, range
- http://partsregistry.org/cd/BBa_B0034, http://purl.org/dc/terms/description, RBS based on Elowitz repressilator
- http://partsregistry.org/cd/BBa_F2620/anno4/range, http://sbols.org/v2#end, 900
- http://partsregistry.org/seq/BBa_C0062, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/seq/BBa_B0034, http://sbols.org/v2#elements, aaagaggagaaa
- http://partsregistry.org/cd/BBa_C0062, http://purl.org/dc/terms/title, BBa_C0062
- http://partsregistry.org/seq/BBa_C0062, http://sbols.org/v2#displayId, BBa_C0062
- http://partsregistry.org/cd/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://partsregistry.org/cd/BBa_F2620/pTetR, http://sbols.org/v2#definition, http://partsregistry.org/cd/BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/rbs, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/rbs
- http://partsregistry.org/seq/BBa_R0062, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/cd/BBa_B0015, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620/rbs, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://sbols.org/v2#end, 956
- http://partsregistry.org/cd/BBa_F2620/anno2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/luxR
- http://partsregistry.org/cd/BBa_C0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_C0062
- http://partsregistry.org/seq/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://partsregistry.org/cd/BBa_R0040, http://purl.org/dc/terms/title, BBa_R0040
- http://partsregistry.org/cd/BBa_F2620/anno3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://partsregistry.org/cd/BBa_F2620/anno4, http://sbols.org/v2#component, http://partsregistry.org/cd/BBa_F2620/ter
- http://partsregistry.org/cd/BBa_F2620/anno5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://partsregistry.org/cd/BBa_F2620/anno5, http://sbols.org/v2#displayId, anno5
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#location, http://partsregistry.org/cd/BBa_F2620/anno2/range
- http://partsregistry.org/cd/BBa_R0062, http://sbols.org/v2#sequence, http://partsregistry.org/seq/BBa_R0062
- http://partsregistry.org/cd/BBa_F2620/pLuxR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://partsregistry.org/cd/BBa_F2620, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#sequenceAnnotation, http://partsregistry.org/cd/BBa_F2620/anno3
- http://partsregistry.org/cd/BBa_F2620, http://sbols.org/v2#displayId, BBa_F2620
- http://partsregistry.org/cd/BBa_F2620/anno1/range, http://sbols.org/v2#start, 1
- http://partsregistry.org/cd/BBa_F2620/anno2, http://sbols.org/v2#persistentIdentity, http://partsregistry.org/cd/BBa_F2620/anno2
- http://partsregistry.org/cd/BBa_F2620/anno3/range, http://sbols.org/v2#start, 69
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#displayId, myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Collection
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/myParts
- http://www.async.ece.utah.edu/myParts/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:29 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:30 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 770,
- Property: components[1].subComponents[0].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:701, Calculated location length:13, Sequence: http://partsregistry.org/seq/BBa_C0062,
- Value: [http://partsregistry.org/cd/BBa_F2620/rbs/range],
- Property: components[1].subComponents[2].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:55, Calculated location length:56, Sequence: http://partsregistry.org/seq/BBa_R0062,
- Value: [http://partsregistry.org/cd/BBa_F2620/pLuxR/range],
- Property: components[1].subComponents[3].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 771,
- Property: components[1].subComponents[1].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 55,
- Property: components[1].subComponents[4].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:129, Calculated location length:130, Sequence: http://partsregistry.org/seq/BBa_B0015,
- Value: [http://partsregistry.org/cd/BBa_F2620/ter/range],
- Property: components[1].subComponents[1].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 901,
- Property: components[1].subComponents[3].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:54, Calculated location length:55, Sequence: http://partsregistry.org/seq/BBa_R0040,
- Value: [http://partsregistry.org/cd/BBa_F2620/pTetR/range],
- Property: components[1].subComponents[4].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 69,
- Property: components[1].subComponents[0].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 56,
- Property: components[1].subComponents[2].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 900,
- Property: components[1].subComponents[1].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/ter/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 68,
- Property: components[1].subComponents[2].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/rbs/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:12, Calculated location length:702, Sequence: http://partsregistry.org/seq/BBa_B0034,
- Value: [http://partsregistry.org/cd/BBa_F2620/luxR/range],
- Property: components[1].subComponents[0].hasLocation,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/luxR,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 956,
- Property: components[1].subComponents[3].locations[0].end,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pLuxR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[1].subComponents[4].locations[0].start,
- Entity URI: http://partsregistry.org/cd/BBa_F2620/pTetR/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0040 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_R0062 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_F2620 differ.
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno5 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno3 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno1 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno2 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/anno4 not found in java32.xml
-->SequenceAnnotation http://partsregistry.org/cd/BBa_F2620/rbs_GenericLocation_anno2 not found in ComponentDefinitionOutput.xml
-ComponentDefinition http://partsregistry.org/cd/BBa_B0034 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_B0015 differ.
-ComponentDefinition http://partsregistry.org/cd/BBa_C0062 differ.
-ComponentDefinition http://www.async.ece.utah.edu/GenericLocationComponent not found in ComponentDefinitionOutput.xml
-Sequence http://partsregistry.org/seq/BBa_R0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0015 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_C0062 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_R0040 not found in java32.xml
-Sequence http://partsregistry.org/seq/BBa_B0034 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
-Python Score = 1
-Java Score = 1
-Number of Files = 13
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml, not in python32.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml:
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:33 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml
-Python Score = 1
-Java Score = 2
-Number of Files = 14
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveComponentDefinition.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveComponentDefinition.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:35 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:36 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveComponentDefinition.xml
-Python Score = 2
-Java Score = 3
-Number of Files = 15
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml, not in python32.xml:
- http://www.async.ece.utah.edu/someGenTopLev/1.0, http://sbols.org/v2#displayId, someGenTopLev
- http://www.async.ece.utah.edu/someGenTopLev/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someGenTopLev
- http://www.async.ece.utah.edu/someGenTopLev/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someGenTopLev/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, urn:bbn.com:tasbe:grn/RegulatoryReaction
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:38 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:39 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml
-Python Score = 2
-Java Score = 4
-Number of Files = 16
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml, not in python32.xml:
- http://www.async.ece.utah.edu/someSequence2/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someSequence3/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someSequence1/1.0, http://sbols.org/v2#version, 1.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml:
- http://www.async.ece.utah.edu/someSequence2/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/someSequence1/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/someSequence3/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:41 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:42 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-10503 - The elements property of a Sequence MUST be consistent with its encoding property.,
- Value: ACGTURYSWKMBDHVN-.,
- Property: sequences[0].elements,
- Entity URI: http://www.async.ece.utah.edu/1.0/someSequence,
- Entity Type: class org.sbolstandard.core3.entity.Sequence
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Collection http://www.async.ece.utah.edu/someSequence1/1.0 not found in java32.xml
-Collection http://www.async.ece.utah.edu/someSequence2/1.0 not found in java32.xml
-Collection http://www.async.ece.utah.edu/someSequence3/1.0 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/someSequence/1.0 not found in java32.xml
-GenericTopLevel http://www.async.ece.utah.edu/someGenTopLev/1.0 not found in CreateAndRemoveModel.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
-Python Score = 2
-Java Score = 4
-Number of Files = 17
-File: /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModuleDefinition.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModuleDefinition.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:44 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:45 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModuleDefinition.xml
-Python Score = 3
-Java Score = 5
-Number of Files = 18
-File: /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 619, in visit_document
- self.visit_activity(obj)
- ~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 528, in visit_activity
- act3.usage = [usage.visit_usage(self) for usage in act2.usages]
- ^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol2/object.py", line 429, in __getattribute__
- result = object.__getattribute__(self, name)
-AttributeError: 'Usage' object has no attribute 'visit_usage'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml, not in python32.xml:
- http://sys-bio.org/Activity_raw_data_generation/1.0.0, http://www.w3.org/ns/prov#qualifiedUsage, http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0
- http://sys-bio.org/Activity_design_generation/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_design_generation
- http://sys-bio.org/Activity_design_generation/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Usage
- http://sys-bio.org/Activity_raw_data_generation/1.0.0, http://sbols.org/v2#displayId, Activity_raw_data_generation
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_fit_model_generation/raw_data_usage
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://sbols.org/v2#displayId, Activity_fit_model_generation
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://www.w3.org/ns/prov#hadRole, http://sbols.org/v2#build
- http://sys-bio.org/Activity_design_generation/1.0.0, http://www.w3.org/ns/prov#qualifiedUsage, http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0
- http://sys-bio.org/Activity_design_generation/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Activity
- http://sys-bio.org/Activity_raw_data_generation/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Usage
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://sbols.org/v2#displayId, build_usage
- http://sys-bio.org/Activity_raw_data_generation/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Activity
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_raw_data_generation/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_raw_data_generation
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://www.w3.org/ns/prov#entity, http://sys-bio.org/Attachment_raw_data/1.0.0
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://sbols.org/v2#displayId, raw_data_usage
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://sbols.org/v2#displayId, predicted_usage
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://www.w3.org/ns/prov#entity, http://sys-bio.org/Implementation_build/1.0.0
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Usage
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_fit_model_generation
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://www.w3.org/ns/prov#hadRole, http://sbols.org/v2#test
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://www.w3.org/ns/prov#entity, http://sys-bio.org/Model_predicted/1.0.0
- http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://sbols.org/v2#version, 1.0.0
- http://sys-bio.org/Activity_design_generation/1.0.0, http://sbols.org/v2#displayId, Activity_design_generation
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_design_generation/predicted_usage
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://purl.org/dc/terms/created, 2003-12-04T12:00:00Z
- http://sys-bio.org/Activity_design_generation/predicted_usage/1.0.0, http://www.w3.org/ns/prov#hadRole, http://sbols.org/v2#learn
- http://sys-bio.org/Activity_raw_data_generation/build_usage/1.0.0, http://sbols.org/v2#persistentIdentity, http://sys-bio.org/Activity_raw_data_generation/build_usage
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.w3.org/ns/prov#Activity
- http://sys-bio.org/Activity_fit_model_generation/1.0.0, http://www.w3.org/ns/prov#qualifiedUsage, http://sys-bio.org/Activity_fit_model_generation/raw_data_usage/1.0.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml:
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#displayId, someModDef
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModDef
- http://www.async.ece.utah.edu/someModDef/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:47 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Activity http://sys-bio.org/Activity_raw_data_generation/1.0.0 not found in java32.xml
-Activity http://sys-bio.org/Activity_design_generation/1.0.0 not found in java32.xml
-Activity http://sys-bio.org/Activity_fit_model_generation/1.0.0 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
-Python Score = 3
-Java Score = 5
-Number of Files = 19
-File: /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml, not in python32.xml:
- http://www.async.ece.utah.edu/EF587312_seq/1, http://sbols.org/v2#elements, gtgattaagcacacaaaggcagcttggagtatgtctgttattaatttcacaggtagttctggtccattggtgaaagtttgcggcttgcagagcacagaggccgcagaatgtgctctagattccgatgctgacttgctgggtattatatgtgtgcccaatagaaagagaacaattgacccggttattgcaaggaaaatttcaagtcttgtaaaagcatataaaaatagttcaggcactccgaaatacttggttggcgtgtttcgtaatcaacctaaggaggatgttttggctctggtcaatgattacggcattgatatcgtccaactgcatggagatgagtcgtggcaagaataccaagagttcctcggtttgccagttattaaaagactcgtatttccaaaagactgcaacatactactcagtgcagcttcacagaaacctcattcgtttattcccttgtttgattcagaagcaggtgggacaggtgaacttttggattggaactcgatttctgactgggttggaaggcaagagagccccgaaagcttacattttatgttagctggtggactgacgccagaaaatgttggtgatgcgcttagattaaatggcgttattggtgttgatgtaagcggaggtgtggagacaaatggtgtaaaagactctaacaaaatagcaaatttcgtcaaaaatgctaagaaatag
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://purl.org/dc/terms/title, TRP1
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.ncbi.nlm.nih.gov/genbank#authors, Zaltsman,A., Yi,B.Y., Krichevsky,A., Gafni,Y. and Citovsky,V.
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#region, complement(1379..2083)
- http://www.async.ece.utah.edu/EF587312/reference1, http://www.ncbi.nlm.nih.gov/genbank#label, 2 (bases 1 to 705)
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/genBankConversion#organism, Yeast expression vector pNIA-Cb
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/EF587312_seq/1, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0002206
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/genBankConversion#db_xref, taxon:443237
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/EF587312/annotation1/range/1
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#keywords, .
- http://www.async.ece.utah.edu/EF587312_seq/1, http://sbols.org/v2#displayId, EF587312_seq
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/EF587312/annotation0/1
- http://www.async.ece.utah.edu/EF587312/reference1, http://www.ncbi.nlm.nih.gov/genbank#authors, Zaltsman,A.A. and Citovsky,V.
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/EF587312_seq/1
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#locus, EF587312
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.ncbi.nlm.nih.gov/genbank#label, 1 (bases 1 to 705)
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/genBankConversion#mol_type, other DNA
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#end, 705
- http://www.async.ece.utah.edu/EF587312/reference1, http://www.ncbi.nlm.nih.gov/genbank#journal, Submitted (27-APR-2007) Biochemistry and Cell Bio, State University of New York, Stony Brook, NY 11777, USA
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ncbi.nlm.nih.gov/genbank#Reference
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#division, SYN
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.ncbi.nlm.nih.gov/genbank#title, Yeast-plant coupled vector system for identification of nuclear proteins
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/EF587312_seq/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312/1, http://purl.obolibrary.org/obo/OBI_0001617, 17704231
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312/annotation1/range
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://purl.org/dc/terms/title, Yeast expression vector pNIA-Cb
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/EF587312/annotation0/range/1
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/genBankConversion#codon_start, 1
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#reference, http://www.async.ece.utah.edu/EF587312/reference0
- http://www.async.ece.utah.edu/EF587312_seq/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#end, 705
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.ncbi.nlm.nih.gov/genbank#pubmed, 17704231
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#source, Yeast expression vector pNIA-Cb
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/genBankConversion#transl_table, 11
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312/annotation0/range
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/EF587312_seq/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312_seq
- http://www.async.ece.utah.edu/EF587312/reference0, http://www.ncbi.nlm.nih.gov/genbank#journal, Plant Physiol. 145 (4), 1264-1271 (2007)
- http://www.async.ece.utah.edu/EF587312/reference1, http://www.ncbi.nlm.nih.gov/genbank#title, Direct Submission
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#reference, http://www.async.ece.utah.edu/EF587312/reference1
- http://www.async.ece.utah.edu/EF587312/reference1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ncbi.nlm.nih.gov/genbank#Reference
- http://www.async.ece.utah.edu/EF587312/annotation0/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312/annotation0
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/EF587312/annotation1
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/genBankConversion#product, TRP1
- http://www.async.ece.utah.edu/EF587312/annotation0/range/1, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/EF587312/annotation1/1
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/genBankConversion#translation, MIKHTKAAWSMSVINFTGSSGPLVKVCGLQSTEAAECALDSDADLLGIICVPNRKRTIDPVIARKISSLVKAYKNSSGTPKYLVGVFRNQPKEDVLALVNDYGIDIVQLHGDESWQEYQEFLGLPVIKRLVFPKDCNILLSAASQKPHSFIPLFDSEAGGTGELLDWNSISDWVGRQESPESLHFMLAGGLTPENVGDALRLNGVIGVDVSGGVETNGVKDSNKIANFVKNAKK
- http://www.async.ece.utah.edu/EF587312/annotation1/range/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/EF587312/1, http://sbols.org/v2#displayId, EF587312
- http://www.async.ece.utah.edu/EF587312/1, http://purl.org/dc/terms/description, Yeast expression vector pNIA-Cb, complete sequence.
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#date, 07-DEC-2007
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#organism, Yeast expression vector pNIA-Cb other sequences; artificial sequences; vectors.
- http://www.async.ece.utah.edu/EF587312/annotation1/1, http://sbols.org/genBankConversion#protein_id, ABQ43169.1
- http://www.async.ece.utah.edu/EF587312/1, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/EF587312/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml:
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#displayId, someModDef
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModDef
- http://www.async.ece.utah.edu/someModDef/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:50 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://www.async.ece.utah.edu/EF587312/1 differ.
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
-Python Score = 3
-Java Score = 5
-Number of Files = 20
-File: /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml, not in python32.xml:
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#sequenceAnnotation, https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1, http://sbols.org/v2#location, https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1, http://sbols.org/v2#displayId, annotation942815
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1, http://sbols.org/v2#persistentIdentity, https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1, http://sbols.org/v2#version, 1
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://michael.zhang/Pro_GeneratedInstance82/1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1, http://sbols.org/v2#version, 1
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#role, http://wiki.synbiohub.org/wiki/Terms/igem#partType/Reporter
- http://michael.zhang/Pro_GeneratedInstance82/1, http://sbols.org/v2#version, 1
- https://synbiohub.org/public/igem/BBa_E0422/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://michael.zhang/Pro_GeneratedInstance82/1, http://sbols.org/v2#displayId, Pro_GeneratedInstance82
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/gl942815/1, http://sbols.org/v2#displayId, gl942815
- http://michael.zhang/Pro_GeneratedInstance82/1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://michael.zhang/Pro_GeneratedInstance82/1, http://sbols.org/v2#persistentIdentity, http://michael.zhang/Pro_GeneratedInstance82
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#persistentIdentity, https://synbiohub.org/public/igem/BBa_E0422
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#version, 1
- https://synbiohub.org/public/igem/BBa_E0422/1, http://sbols.org/v2#displayId, BBa_E0422
- https://synbiohub.org/public/igem/BBa_E0422/annotation942815/1, http://sbols.org/v2#persistentIdentity, https://synbiohub.org/public/igem/BBa_E0422/annotation942815
- http://michael.zhang/Pro_GeneratedInstance82/1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml:
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModDef
- http://www.async.ece.utah.edu/someModDef/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someModDef/1.0, http://sbols.org/v2#displayId, someModDef
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:52 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:52 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition https://synbiohub.org/public/igem/BBa_E0422/1 differ.
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
-Python Score = 3
-Java Score = 5
-Number of Files = 21
-File: /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml, not in python32.xml:
- http://www.partsregistry.org/gen/datasheet1, http://sbols.org/v2#displayId, datasheet1
- http://www.partsregistry.org/gen/datasheet1, http://purl.org/dc/terms/title, Datasheet 1
- http://www.partsregistry.org/gen/datasheet1, http://www.myapp.org/characterizationData, http://www.myapp.org//measurement/1
- http://www.partsregistry.org/gen/datasheet1, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/gen/datasheet1
- http://www.partsregistry.org/gen/datasheet1, http://www.myapp.org/transcriptionRate, 1
- http://www.partsregistry.org/gen/datasheet1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.myapp.org/Datasheet
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:55 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:55 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml
-Python Score = 3
-Java Score = 6
-Number of Files = 22
-File: /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml, not in python32.xml:
- http://www.partsregistry.org/gen/datasheet1, http://www.myapp.org/transcriptionRate, 1
- http://www.partsregistry.org/gen/datasheet1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.myapp.org/Datasheet
- http://www.partsregistry.org/gen/datasheet1, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/gen/datasheet1
- http://www.partsregistry.org/gen/datasheet1, http://sbols.org/v2#displayId, datasheet1
- http://www.partsregistry.org/gen/datasheet1, http://www.myapp.org/characterizationData, http://www.myapp.org//measurement/1
- http://www.partsregistry.org/gen/datasheet1, http://purl.org/dc/terms/title, Datasheet 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:57 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:15:58 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml
-Python Score = 3
-Java Score = 7
-Number of Files = 23
-File: /Users/myers/git/SBOLTestSuite/SBOL2/implementation_example.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/implementation_example.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:16:00 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:16:01 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/implementation_example.xml
-Python Score = 4
-Java Score = 8
-Number of Files = 24
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_All.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_All.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Insect_Cells
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Saccharomyces_cerevisiae
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Bacillus_subtilis
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Unspecified_labhost
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Aspergillus_nidulans
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Schizosaccharomyces_pombe
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Escherichia_Coli
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Kluyveromyces_lactis
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Pichia_pastoris
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Gram_negative_bacteria
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Plant_Cells
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Drosophila_melanogaster
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Mammalian_Cells
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_All.xml:
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_All.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:05 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:08 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_All.xml
-Python Score = 4
-Java Score = 9
-Number of Files = 25
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Aspergillus_nidulans
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml:
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Aspergillus_nidulans, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:29 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:30 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml
-Python Score = 4
-Java Score = 10
-Number of Files = 26
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Bacillus_subtilis
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml:
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Bacillus_subtilis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:33 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml
-Python Score = 4
-Java Score = 11
-Number of Files = 27
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Drosophila_melanogaster
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml:
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Drosophila_melanogaster, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:35 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:36 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml
-Python Score = 4
-Java Score = 12
-Number of Files = 28
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Escherichia_Coli
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml:
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Escherichia_Coli, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:48 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml
-Python Score = 4
-Java Score = 13
-Number of Files = 29
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Gram_negative_bacteria
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml:
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Gram_negative_bacteria, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:54 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:55 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml
-Python Score = 4
-Java Score = 14
-Number of Files = 30
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Insect_Cells
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml:
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Insect_Cells, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:17:59 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:00 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml
-Python Score = 4
-Java Score = 15
-Number of Files = 31
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Kluyveromyces_lactis
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml:
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Kluyveromyces_lactis, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:03 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:04 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml
-Python Score = 4
-Java Score = 16
-Number of Files = 32
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Mammalian_Cells
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml:
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Mammalian_Cells, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:18 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:20 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml
-Python Score = 4
-Java Score = 17
-Number of Files = 33
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Pichia_pastoris
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml:
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Pichia_pastoris, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:26 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:27 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml
-Python Score = 4
-Java Score = 18
-Number of Files = 34
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Plant_Cells
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml:
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Plant_Cells, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:31 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml
-Python Score = 4
-Java Score = 19
-Number of Files = 35
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Saccharomyces_cerevisiae
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml:
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Saccharomyces_cerevisiae, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:36 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:37 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml
-Python Score = 4
-Java Score = 20
-Number of Files = 36
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Schizosaccharomyces_pombe
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml:
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
- http://www.async.ece.utah.edu/Schizosaccharomyces_pombe, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:40 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:40 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml
-Python Score = 4
-Java Score = 21
-Number of Files = 37
-File: /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Unspecified.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Unspecified.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Unspecified_labhost
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Unspecified.xml:
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/Unspecified_labhost, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Unspecified.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:46 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:47 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/labhost_Unspecified.xml
-Python Score = 4
-Java Score = 22
-Number of Files = 38
-File: /Users/myers/git/SBOLTestSuite/SBOL2/manifest
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/usr/local/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/xml/sax/expatreader.py", line 211, in feed
- self._parser.Parse(data, isFinal)
- ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
-xml.parsers.expat.ExpatError: syntax error: line 1, column 0
-
-During handling of the above exception, another exception occurred:
-
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 419, in command_line_converter
- doc2.read(input_file)
- ~~~~~~~~~^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol2/document.py", line 426, in read
- self.append(filename, overwrite=False)
- ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol2/document.py", line 463, in append
- new_graph.parse(filename, format='application/rdf+xml')
- ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/graph.py", line 1494, in parse
- parser.parse(source, self, **args)
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/rdfxml.py", line 647, in parse
- self._parser.parse(source)
- ~~~~~~~~~~~~~~~~~~^^^^^^^^
- File "/usr/local/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/xml/sax/expatreader.py", line 105, in parse
- xmlreader.IncrementalParser.parse(self, source)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
- File "/usr/local/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/xml/sax/xmlreader.py", line 124, in parse
- self.feed(buffer)
- ~~~~~~~~~^^^^^^^^
- File "/usr/local/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/xml/sax/expatreader.py", line 215, in feed
- self._err_handler.fatalError(exc)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/usr/local/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/xml/sax/handler.py", line 38, in fatalError
- raise exception
-xml.sax._exceptions.SAXParseException: file:///Users/myers/git/SBOLTestSuite/SBOL2/manifest:1:0: syntax error
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/graph.py", line 1494, in parse
- parser.parse(source, self, **args)
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 2021, in parse
- p.loadStream(stream)
- ~~~~~~~~~~~~^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 479, in loadStream
- return self.loadBuf(stream.read()) # Not ideal
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 485, in loadBuf
- self.feed(buf)
- ~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 514, in feed
- self.BadSyntax(s, j, "expected directive or statement")
- ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 1730, in BadSyntax
- raise BadSyntax(self._thisDoc, self.lines, argstr, i, msg)
-rdflib.plugins.parsers.notation3.BadSyntax:
-
-During handling of the above exception, another exception occurred:
-
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-diff", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 235, in main
- return file_diff(args.file1, args.file2, silent=args.silent,
- strip_backport_properties=args.strip_backport_properties)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 185, in file_diff
- return _diff_rdf(fpath1, _load_rdf(fpath1), fpath2, _load_rdf(fpath2), silent=silent,
- ~~~~~~~~~^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 25, in _load_rdf
- graph1.parse(fpath, format=rdf_format)
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/graph.py", line 1497, in parse
- raise ParserError(
- ...<3 lines>...
- )
-rdflib.exceptions.ParserError: Could not guess RDF format for <_io.BufferedReader name='/Users/myers/git/SBOLTestSuite/SBOL2/manifest'> from file extension so tried Turtle but failed.You can explicitly specify format using the format argument.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:51 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-sbol-10105: Strong Validation Error:
-An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/”
- Reference: SBOL Version 2.3.0 Section 10 on page 58
-Validation failed.
-Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.util.List.size()" because the return value of "org.sbolstandard.core2.SBOLValidate.getErrors()" is null
- at org.sbolstandard.converter.App.main(App.java:265)
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
-Python Score = 4
-Java Score = 22
-Number of Files = 39
-File: /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml, not in python32.xml:
- http://www.async.ece.utah.edu/md/fc, http://sbols.org/v2#measure, http://www.async.ece.utah.edu/md/fc/fc_measure
- http://www.async.ece.utah.edu/md/m/md_measure, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/md/m/md_measure
- http://www.async.ece.utah.edu/md/i/p/pMeasure, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ontology-of-units-of-measure.org/resource/om-2/Measure
- http://www.async.ece.utah.edu/md/i/p, http://sbols.org/v2#measure, http://www.async.ece.utah.edu/md/i/p/pMeasure
- http://www.async.ece.utah.edu/md/m, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/md/m
- http://www.async.ece.utah.edu/md/m/md_measure, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ontology-of-units-of-measure.org/resource/om-2/Measure
- http://www.async.ece.utah.edu/md/m, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.async.ece.utah.edu/md/i/p/pMeasure, http://sbols.org/v2#displayId, pMeasure
- http://www.async.ece.utah.edu/md/m, http://sbols.org/v2#measure, http://www.async.ece.utah.edu/md/m/md_measure
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit, http://purl.obolibrary.org/obo/UO_0000021
- http://www.async.ece.utah.edu/md/i/i_measure, http://sbols.org/v2#displayId, i_measure
- http://www.async.ece.utah.edu/md/m/md_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit, http://purl.obolibrary.org/obo/UO_0000175
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://sbols.org/v2#type, http://identifiers.org/biomodels.sbo/SBO:0000610
- http://www.async.ece.utah.edu/md/i/p/pMeasure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit, http://purl.obolibrary.org/obo/UO_0000021
- http://www.async.ece.utah.edu/md/m, http://sbols.org/v2#displayId, m
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ontology-of-units-of-measure.org/resource/om-2/Measure
- http://www.async.ece.utah.edu/md/i/i_measure, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://www.ontology-of-units-of-measure.org/resource/om-2/Measure
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/md/fc/fc_measure
- http://www.async.ece.utah.edu/md/i/i_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasUnit, http://purl.obolibrary.org/obo/UO_0000077
- http://www.async.ece.utah.edu/md/i/p/pMeasure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue, 1.23
- http://www.async.ece.utah.edu/md, http://sbols.org/v2#module, http://www.async.ece.utah.edu/md/m
- http://www.async.ece.utah.edu/md/i, http://sbols.org/v2#measure, http://www.async.ece.utah.edu/md/i/i_measure
- http://www.async.ece.utah.edu/md/m, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/empty_md
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://sbols.org/v2#displayId, fc_measure
- http://www.async.ece.utah.edu/md/i/i_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue, 0.04
- http://www.async.ece.utah.edu/md/m/md_measure, http://sbols.org/v2#displayId, md_measure
- http://www.async.ece.utah.edu/md/fc/fc_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue, 0.04
- http://www.async.ece.utah.edu/md/i/p/pMeasure, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/md/i/p/pMeasure
- http://www.async.ece.utah.edu/md/m/md_measure, http://www.ontology-of-units-of-measure.org/resource/om-2/hasNumericalValue, 11.28
- http://www.async.ece.utah.edu/md/i/i_measure, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/md/i/i_measure
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:53 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:54 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ModuleDefinition http://www.async.ece.utah.edu/md differ.
-->FunctionalComponent http://www.async.ece.utah.edu/md/fc differ.
----->Measure http://www.async.ece.utah.edu/md/fc/fc_measure not found in java32.xml
-->Module http://www.async.ece.utah.edu/md/m differ.
----->Measure http://www.async.ece.utah.edu/md/m/md_measure not found in java32.xml
-->Interaction http://www.async.ece.utah.edu/md/i differ.
----->Measure http://www.async.ece.utah.edu/md/i/i_measure not found in java32.xml
---->Participation http://www.async.ece.utah.edu/md/i/p differ.
----->Measure http://www.async.ece.utah.edu/md/i/p/pMeasure not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
-Python Score = 4
-Java Score = 22
-Number of Files = 40
-File: /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_int_md.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_int_md.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:57 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:57 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_int_md.xml
-Python Score = 5
-Java Score = 23
-Number of Files = 41
-File: /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml, not in python32.xml:
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/someModuleDefSub/1.0
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#module, http://www.async.ece.utah.edu/someModuleDef/someModule/1.0
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#displayId, someModule
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDef/someModule
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:18:59 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:00 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml
-Python Score = 5
-Java Score = 24
-Number of Files = 42
-File: /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:02 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:03 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_ann.xml
-Python Score = 6
-Java Score = 25
-Number of Files = 43
-File: /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml, not in python32.xml:
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDef/someModule
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/someModuleDefSub/1.0
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#module, http://www.async.ece.utah.edu/someModuleDef/someModule/1.0
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#displayId, someModule
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:05 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:06 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml
-Python Score = 6
-Java Score = 26
-Number of Files = 44
-File: /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml, not in python32.xml:
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://sbols.org/v2#end, 10
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/someCompDefCDS/1.0
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#language, http://identifiers.org/edam/format_2585
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#displayId, someModule
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://sbols.org/v2#displayId, someCompDefCDS
- http://www.async.ece.utah.edu/someGenericTopLevel/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0, http://sbols.org/v2#type, http://identifiers.org/biomodels.sbo/SBO:0000177
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDef/someModule
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#component, http://www.async.ece.utah.edu/someCompDef/someComponent/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someOtherComponent
- http://www.async.ece.utah.edu/someSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/someCompDefCDS/1.0
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#module, http://www.async.ece.utah.edu/someModuleDef/someModule/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#displayId, myParts
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#displayId, someCompDef
- http://www.async.ece.utah.edu/someGenericTopLevel/1.0, http://sbols.org/v2#displayId, someGenericTopLevel
- http://www.async.ece.utah.edu/someSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/someCompDef/someComponent/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0, http://sbols.org/v2#displayId, someSequenceAnnotation2
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://sbols.org/v2#displayId, someComponent
- http://www.async.ece.utah.edu/someModel/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Model
- http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0
- http://www.async.ece.utah.edu/someGenericTopLevel/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someGenericTopLevel
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#framework, http://identifiers.org/biomodels.sbo/SBO:0000062
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#component, http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0
- http://www.async.ece.utah.edu/someSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/someModuleDef/someModule/1.0, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/someModuleDefSub/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/myParts/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/myParts
- http://www.async.ece.utah.edu/someCompDef/someComponent/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someComponent
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0
- http://www.async.ece.utah.edu/someGenericTopLevel/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2
- http://www.async.ece.utah.edu/someGenericTopLevel/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, urn:bbn.com:tasbe:grn/RegulatoryReaction
- http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0, http://sbols.org/v2#displayId, someInteraction
- http://www.async.ece.utah.edu/someSeq/1.0, http://sbols.org/v2#displayId, someSeq
- http://www.async.ece.utah.edu/myParts/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDef/someInteraction
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/myParts/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Collection
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#displayId, someModel
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://sbols.org/v2#displayId, someSequenceAnnotation
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://sbols.org/v2#displayId, cut
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#interaction, http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0
- http://www.async.ece.utah.edu/someSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someSeq
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://sbols.org/v2#at, 1
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/1.0
- http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0, http://sbols.org/v2#displayId, someOtherComponent
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#source, file:///Users/myers/git/SBOLTestSuite/SBOL2/someModel_source
- http://www.async.ece.utah.edu/someCompDef/1.0, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0
- http://www.async.ece.utah.edu/someSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/someSeq/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someModel/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModel
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Cut
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Interaction
- http://www.async.ece.utah.edu/someCompDef/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation2/cut/1.0, http://sbols.org/v2#displayId, cut
- http://www.async.ece.utah.edu/someCompDefCDS/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someCompDefCDS
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#object, http://www.async.ece.utah.edu/someCompDef/someOtherComponent/1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceConstraint/1.0, http://sbols.org/v2#displayId, someSequenceConstraint
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/cut/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someCompDef/someSequenceAnnotation/1.0, http://myannotation.org/thisAnnotation, turtleString
- http://www.async.ece.utah.edu/someModel/1.0, http://myannotation.org/thisAnnotation, turtleString
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:08 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:09 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11501 - The value of the at property of a Cut MUST be greater than or equal to zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[1].sequenceFeatures[1].locations[0].at,
- Entity URI: http://www.async.ece.utah.edu/1.0/someCompDef/someSequenceAnnotation2/cut,
- Entity Type: class org.sbolstandard.core3.entity.Cut
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[1].sequenceFeatures[0].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/1.0/someCompDef/someSequenceAnnotation/cut,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 10,
- Property: components[1].sequenceFeatures[0].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/1.0/someCompDef/someSequenceAnnotation/cut,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10503 - The elements property of a Sequence MUST be consistent with its encoding property.,
- Value: ACGTURYSWKMBDHVN-.,
- Property: sequences[0].elements,
- Entity URI: http://www.async.ece.utah.edu/1.0/someSeq,
- Entity Type: class org.sbolstandard.core3.entity.Sequence
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Collection http://www.async.ece.utah.edu/myParts/1.0 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/someCompDef/1.0 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/someCompDefCDS/1.0 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/someSeq/1.0 not found in java32.xml
-ModuleDefinition http://www.async.ece.utah.edu/someModuleDef/1.0 differ.
-->Interaction http://www.async.ece.utah.edu/someModuleDef/someInteraction/1.0 not found in java32.xml
-Model http://www.async.ece.utah.edu/someModel/1.0 not found in java32.xml
-GenericTopLevel http://www.async.ece.utah.edu/someGenericTopLevel/1.0 not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
-Python Score = 6
-Java Score = 26
-Number of Files = 45
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ModelOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 613, in visit_document
- self.visit_model(obj)
- ~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 679, in visit_model
- raise NotImplementedError('Conversion of Model from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of Model from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ModelOutput.xml, not in python32.xml:
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://sbols.org/v2#displayId, pIKE_Toggle_1
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://purl.org/dc/terms/title, pIKE_Toggle_1 toggle switch
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://sbols.org/v2#source, http://virtualparts.org/part/pIKE_Toggle_1
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Model
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://sbols.org/v2#language, http://identifiers.org/edam/format_2585
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://sbols.org/v2#persistentIdentity, http://www.sbolstandard.org/examples/pIKE_Toggle_1
- http://www.sbolstandard.org/examples/pIKE_Toggle_1, http://sbols.org/v2#framework, http://identifiers.org/biomodels.sbo/SBO:0000062
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ModelOutput.xml:
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#displayId, someModuleDef
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someModuleDefSub/1.0, http://sbols.org/v2#displayId, someModuleDefSub
- http://www.async.ece.utah.edu/someModuleDefSub/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://www.async.ece.utah.edu/someModuleDefSub/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDef
- http://www.async.ece.utah.edu/someModuleDefSub/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/someModuleDefSub
- http://www.async.ece.utah.edu/someModuleDef/1.0, http://myannotation.org/thisAnnotation, turtleString
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModelOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:11 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:12 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/ModelOutput.xml
-Python Score = 6
-Java Score = 27
-Number of Files = 46
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput_int_md_ann.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput_int_md_ann.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:14 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:14 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput_int_md_ann.xml
-Python Score = 7
-Java Score = 28
-Number of Files = 47
-File: /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 781, in visit_sequence_annotation
- l3 = self.visit_range(l2)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 755, in visit_range
- cdef.sequence = seq_stup
- ^^^^^^^^
-NameError: name 'seq_stup' is not defined. Did you mean: 'seq_stub'?
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml, not in python32.xml:
- http://sbolstandard.org/example/tetr_inverter/TF, http://sbols.org/v2#displayId, TF
- http://www.partsregistry.org/BBa_J61101, http://purl.org/dc/terms/description, RBS1
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1, http://sbols.org/v2#displayId, pIKELeftCassette_1
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://sbols.org/v2#start, 1464
- http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736, http://sbols.org/v2#definition, http://www.partsregistry.org/ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_C0012
- http://identifiers.org/uniprot/P03023, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#Protein
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://identifiers.org/uniprot/Q6QR72, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://identifiers.org/uniprot/Q6QR72, http://sbols.org/v2#displayId, Q6QR72
- http://www.partsregistry.org/BBa_J61130, http://sbols.org/v2#displayId, BBa_J61130
- http://www.partsregistry.org/BBa_J61130, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_J61130
- http://www.partsregistry.org/BBa_C0012, http://purl.org/dc/terms/description, lacI coding sequence
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKE_Toggle_1/anno1
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72, http://sbols.org/v2#participant, http://sbolstandard.org/example/tetr_inverter/TF
- http://www.partsregistry.org/ECK120033736, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_C0012
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno6
- http://www.partsregistry.org/ECK120033736, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://sbols.org/v2#start, 1
- http://www.partsregistry.org/BBa_C0040, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_C0040
- http://www.virtualparts.org/part/BBa_C0012, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://sbols.org/v2#end, 68
- http://www.virtualparts.org/part/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_C0040
- http://identifiers.org/uniprot/P42212, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000011
- http://www.partsregistry.org/BBa_J61130, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012
- http://www.virtualparts.org/part/BBa_J61101, http://sbols.org/v2#displayId, BBa_J61101
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.partsregistry.org/ECK120029600, http://purl.org/dc/terms/description, Terminator1
- http://www.partsregistry.org/BBa_R0040, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_R0040
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://sbols.org/v2#local, http://sbolstandard.org/example/toggle_switch/LacI
- http://www.virtualparts.org/part/BBa_J61130, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/BBa_C0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.partsregistry.org/ECK120033736, http://purl.org/dc/terms/title, ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600
- http://www.partsregistry.org/BBa_J61120, http://purl.org/dc/terms/title, BBa_J61101 RBS
- http://www.virtualparts.org/part/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_R0040
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://sbols.org/v2#refinement, http://sbols.org/v2#useRemote
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://purl.org/dc/terms/title, TetR Inverter
- http://sbolstandard.org/example/toggle_switch, http://sbols.org/v2#model, http://sbolstandard.org/example/toogleswicth
- http://sbolstandard.org/example/tetr_inverter/promoter, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120
- http://www.partsregistry.org/BBa_J61120, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_J61120
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4, http://sbols.org/v2#displayId, anno4
- http://sbolstandard.org/example/tetr_inverter, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/tetr_inverter/promoter
- http://www.partsregistry.org/BBa_R0040, http://purl.org/dc/terms/description, pTet promoter
- http://www.virtualparts.org/part/ECK120033736, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.partsregistry.org/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_E0040
- http://www.partsregistry.org/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#displayId, laci_inverter
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://sbols.org/v2#displayId, location2
- http://identifiers.org/uniprot/P03023, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://sbols.org/v2#end, 55
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6, http://sbols.org/v2#displayId, anno6
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2, http://sbols.org/v2#displayId, anno2
- http://www.partsregistry.org/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://sbolstandard.org/example/toggle_switch/laci_inverter, http://sbols.org/v2#mapsTo, http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000598
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter
- http://www.partsregistry.org/BBa_R0010, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_R0010
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://sbols.org/v2#end, 1285
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://sbols.org/v2#start, 1
- http://identifiers.org/uniprot/Q6QR72, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#Protein
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://sbols.org/v2#start, 56
- http://www.partsregistry.org/BBa_E0040, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_E0040
- http://www.virtualparts.org/part/BBa_E0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://sbolstandard.org/example/laci_inverter/promoter, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter/promoter
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72, http://sbols.org/v2#displayId, Q6QR72
- http://www.virtualparts.org/part/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000020
- http://sbolstandard.org/example/tetr_inverter, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/tetr_inverter/TF
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://sbols.org/v2#start, 743
- http://sbolstandard.org/example/toggle_switch/tetr_inverter, http://sbols.org/v2#definition, http://sbolstandard.org/example/tetr_inverter
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://sbols.org/v2#displayId, location2
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2, http://sbols.org/v2#displayId, anno2
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://sbols.org/v2#remote, http://sbolstandard.org/example/laci_inverter/TF
- http://www.partsregistry.org/ECK120033736, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/ECK120033736
- http://sbolstandard.org/example/tetr_inverter/promoter, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/tetr_inverter/promoter
- http://identifiers.org/uniprot/P42212, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#Protein
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://sbols.org/v2#refinement, http://sbols.org/v2#useRemote
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2
- http://www.partsregistry.org/BBa_C0040, http://purl.org/dc/terms/description, tetR coding sequence
- http://www.partsregistry.org/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://identifiers.org/uniprot/P42212, http://purl.org/dc/terms/title, GFP
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130
- http://www.virtualparts.org/part/BBa_J61101, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_C0040
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://sbols.org/v2#displayId, location3
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000020
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKERightCassette_1, http://purl.org/dc/terms/title, LacI Inverter
- http://www.virtualparts.org/part/ECK120029600, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/ECK120029600
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1
- http://www.virtualparts.org/part/BBa_J61130, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_J61130
- http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/ECK120029600, http://sbols.org/v2#displayId, ECK120029600
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://sbolstandard.org/example/toggle_switch, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/toggle_switch/LacI
- http://www.virtualparts.org/part/ECK120033736, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010
- http://www.partsregistry.org/BBa_C0012, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI, http://sbols.org/v2#participation, http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1, http://sbols.org/v2#definition, http://www.virtualparts.org/part/pIKELeftCassette_1
- http://sbolstandard.org/example/toggle_switch/laci_inverter, http://sbols.org/v2#displayId, laci_inverter
- http://www.virtualparts.org/part/BBa_J61120, http://sbols.org/v2#displayId, BBa_J61120
- http://www.virtualparts.org/part/ECK120033736, http://sbols.org/v2#elements, ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa
- http://identifiers.org/uniprot/P03023, http://purl.org/dc/terms/title, LacI
- http://sbolstandard.org/example/toogleswicth, http://sbols.org/v2#source, http://virtualparts.org/part/pIKE_Toggle_1
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://sbolstandard.org/example/laci_inverter/TF, http://sbols.org/v2#displayId, TF
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKELeftCassette_1/anno4
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010
- http://www.partsregistry.org/BBa_R0040, http://purl.org/dc/terms/title, pTetR
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://sbols.org/v2#displayId, location4
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://sbols.org/v2#displayId, location5
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000280
- http://www.partsregistry.org/BBa_C0012, http://purl.org/dc/terms/title, lacI
- http://www.virtualparts.org/part/pIKERightCassette_1, http://purl.org/dc/terms/description, LacI Inverter
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://sbols.org/v2#displayId, location3
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1, http://sbols.org/v2#displayId, anno1
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKE_Toggle_1/anno2
- http://identifiers.org/uniprot/P03023, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000020
- http://www.virtualparts.org/part/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040, http://sbols.org/v2#participant, http://sbolstandard.org/example/tetr_inverter/promoter
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_J61120
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://sbols.org/v2#displayId, location1
- http://sbolstandard.org/example/tetr_inverter/TF, http://sbols.org/v2#definition, http://identifiers.org/uniprot/Q6QR72
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://sbols.org/v2#displayId, location1
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Interaction
- http://identifiers.org/uniprot/P42212, http://sbols.org/v2#displayId, P42212
- http://www.virtualparts.org/part/BBa_R0010, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101
- http://sbolstandard.org/example/toogleswicth, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toogleswicth
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Participation
- http://www.partsregistry.org/BBa_C0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.partsregistry.org/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023, http://sbols.org/v2#participant, http://sbolstandard.org/example/laci_inverter/TF
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.partsregistry.org/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_R0040
- http://sbolstandard.org/example/toggle_switch/LacI, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/LacI
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno2
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#displayId, pIKE_Toggle_1
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno3
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.partsregistry.org/ECK120033736, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.partsregistry.org/BBa_J61120, http://purl.org/dc/terms/description, RBS2
- http://www.partsregistry.org/BBa_E0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://sbolstandard.org/example/laci_inverter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ModuleDefinition
- http://sbolstandard.org/example/tetr_inverter/TF, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/tetr_inverter/TF
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://sbolstandard.org/example/tetr_inverter/TF, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://sbols.org/v2#end, 1463
- http://www.partsregistry.org/BBa_J61101, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.partsregistry.org/BBa_R0010, http://purl.org/dc/terms/description, pLacI promoter
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://sbols.org/v2#end, 1288
- http://www.partsregistry.org/ECK120029600, http://purl.org/dc/terms/title, ECK120029600
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://sbols.org/v2#displayId, TetR_mapping
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3
- http://sbolstandard.org/example/toggle_switch/tetr_inverter, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/tetr_inverter
- http://sbolstandard.org/example/toogleswicth, http://sbols.org/v2#framework, http://identifiers.org/biomodels.sbo/SBO:0000062
- http://www.partsregistry.org/BBa_J61120, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.partsregistry.org/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_C0040
- http://www.virtualparts.org/part/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_E0040
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter/LacI_pLacI
- http://www.virtualparts.org/part/BBa_J61120, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_J61120
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://identifiers.org/uniprot/Q6QR72, http://purl.org/dc/terms/title, TetR
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://sbols.org/v2#remote, http://sbolstandard.org/example/tetr_inverter/TF
- http://www.partsregistry.org/BBa_C0012, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://sbolstandard.org/example/toggle_switch, http://sbols.org/v2#module, http://sbolstandard.org/example/toggle_switch/tetr_inverter
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://sbols.org/v2#participation, http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010
- http://www.partsregistry.org/BBa_J61130, http://purl.org/dc/terms/title, BBa_J61101 RBS
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno4
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_R0010
- http://www.partsregistry.org/ECK120033736, http://purl.org/dc/terms/description, Terminator2
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1, http://sbols.org/v2#displayId, pIKERightCassette_1
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://sbolstandard.org/example/laci_inverter/TF, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter/TF
- http://www.partsregistry.org/BBa_E0040, http://purl.org/dc/terms/title, gfp
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://sbolstandard.org/example/laci_inverter/TF, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://sbolstandard.org/example/tetr_inverter/TF, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI, http://sbols.org/v2#participation, http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040
- http://sbolstandard.org/example/toggle_switch/tetr_inverter, http://sbols.org/v2#displayId, tetr_inverter
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://sbols.org/v2#start, 69
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#displayId, pIKELeftCassette_1
- http://identifiers.org/uniprot/Q6QR72, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000020
- http://www.virtualparts.org/part/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4, http://sbols.org/v2#displayId, anno4
- http://www.virtualparts.org/part/BBa_C0012, http://sbols.org/v2#elements, atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.virtualparts.org/part/ECK120029600, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.virtualparts.org/part/BBa_R0040, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040
- http://www.partsregistry.org/BBa_J61130, http://purl.org/dc/terms/description, RBS2
- http://sbolstandard.org/example/toggle_switch, http://sbols.org/v2#module, http://sbolstandard.org/example/toggle_switch/laci_inverter
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000280
- http://www.virtualparts.org/part/ECK120029600, http://sbols.org/v2#elements, ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa
- http://www.virtualparts.org/part/ECK120033736, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012
- http://www.virtualparts.org/part/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/BBa_J61101, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.partsregistry.org/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://sbolstandard.org/example/toggle_switch/tetr_inverter, http://sbols.org/v2#mapsTo, http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping
- http://www.partsregistry.org/BBa_J61130, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://sbolstandard.org/example/tetr_inverter/TF, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://sbolstandard.org/example/laci_inverter/TF, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://sbolstandard.org/example/toggle_switch/laci_inverter, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/laci_inverter
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Participation
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://sbols.org/v2#start, 1
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKELeftCassette_1/anno2
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6
- http://www.partsregistry.org/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1
- http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736, http://sbols.org/v2#displayId, ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://sbols.org/v2#start, 69
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://sbols.org/v2#end, 68
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040
- http://www.virtualparts.org/part/BBa_J61101, http://sbols.org/v2#elements, aaagacaggacc
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012
- http://www.partsregistry.org/BBa_J61101, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_J61101
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1
- http://sbolstandard.org/example/toggle_switch/LacI, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.partsregistry.org/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://sbols.org/v2#end, 2834
- http://sbolstandard.org/example/toogleswicth, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Model
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno4
- http://www.virtualparts.org/part/BBa_E0040, http://sbols.org/v2#elements, atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa
- http://identifiers.org/uniprot/P42212, http://purl.org/dc/terms/description, GFP protein
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1, http://sbols.org/v2#definition, http://www.virtualparts.org/part/pIKERightCassette_1
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4
- http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600, http://sbols.org/v2#displayId, ECK120029600
- http://www.partsregistry.org/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://sbols.org/v2#type, http://identifiers.org/biomodels.sbo/SBO:0000169
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno6
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#displayId, pIKERightCassette_1
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040
- http://www.virtualparts.org/part/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.partsregistry.org/BBa_J61101, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_J61101
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno5
- http://sbolstandard.org/example/laci_inverter/promoter, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/anno1
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://sbols.org/v2#participation, http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023
- http://sbolstandard.org/example/toggle_switch/TetR, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://purl.org/dc/terms/description, LacI/TetR Toggle Swicth
- http://www.virtualparts.org/part/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_R0010
- http://www.virtualparts.org/part/BBa_R0010, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://identifiers.org/uniprot/P42212, http://sbols.org/v2#persistentIdentity, http://identifiers.org/uniprot/P42212
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno3
- http://www.partsregistry.org/BBa_J61101, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.partsregistry.org/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000280
- http://sbolstandard.org/example/toggle_switch/LacI, http://sbols.org/v2#definition, http://identifiers.org/uniprot/P03023
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010, http://sbols.org/v2#role, http://identifiers.org/biomodels.sbo/SBO:0000598
- http://www.partsregistry.org/BBa_R0010, http://purl.org/dc/terms/title, pLacI
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.partsregistry.org/BBa_C0012, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_C0012
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Participation
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://purl.org/dc/terms/title, LacI/TetR Toggle Swicth
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno4
- http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.partsregistry.org/BBa_J61120, http://sbols.org/v2#displayId, BBa_J61120
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://sbols.org/v2#end, 1554
- http://www.partsregistry.org/BBa_J61101, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://sbols.org/v2#displayId, location2
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130
- http://www.virtualparts.org/part/BBa_J61130, http://sbols.org/v2#displayId, BBa_J61130
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_R0040
- http://www.partsregistry.org/BBa_J61120, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/ECK120029600, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.partsregistry.org/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://sbolstandard.org/example/toggle_switch, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/toggle_switch/TetR
- http://www.virtualparts.org/part/BBa_J61130, http://sbols.org/v2#elements, aaagaaacgaca
- http://www.partsregistry.org/ECK120029600, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/ECK120029600
- http://sbolstandard.org/example/laci_inverter/promoter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://sbolstandard.org/example/toggle_switch/TetR, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://sbolstandard.org/example/toggle_switch/LacI, http://sbols.org/v2#displayId, LacI
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/laci_inverter/promoter
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1
- http://sbolstandard.org/example/toggle_switch/laci_inverter, http://sbols.org/v2#definition, http://sbolstandard.org/example/laci_inverter
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120, http://sbols.org/v2#displayId, BBa_J61120
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://purl.org/dc/terms/description, TetR Inverter
- http://sbolstandard.org/example/toggle_switch/TetR, http://sbols.org/v2#definition, http://identifiers.org/uniprot/Q6QR72
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_J61130
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72
- http://www.virtualparts.org/part/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_E0040
- http://www.partsregistry.org/ECK120033736, http://sbols.org/v2#displayId, ECK120033736
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKELeftCassette_1/anno3
- http://www.partsregistry.org/ECK120029600, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1
- http://www.partsregistry.org/BBa_J61120, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_J61120
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1/location1, http://sbols.org/v2#end, 55
- http://identifiers.org/uniprot/P03023, http://purl.org/dc/terms/description, LacI protein
- http://www.virtualparts.org/part/ECK120033736, http://sbols.org/v2#displayId, ECK120033736
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://sbolstandard.org/example/laci_inverter/promoter, http://sbols.org/v2#displayId, promoter
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://sbols.org/v2#displayId, location6
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI, http://sbols.org/v2#displayId, LacI_pLacI
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://sbols.org/v2#start, 56
- http://sbolstandard.org/example/toggle_switch/tetr_inverter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.partsregistry.org/BBa_J61101, http://sbols.org/v2#displayId, BBa_J61101
- http://sbolstandard.org/example/toggle_switch/TetR, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://sbolstandard.org/example/toggle_switch/LacI, http://sbols.org/v2#direction, http://sbols.org/v2#inout
- http://sbolstandard.org/example/laci_inverter/promoter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://sbols.org/v2#end, 729
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#role, http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#MapsTo
- http://www.virtualparts.org/part/pIKE_Toggle_1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://sbolstandard.org/example/tetr_inverter/promoter, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_R0040
- http://www.virtualparts.org/part/BBa_R0040, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.virtualparts.org/part/BBa_J61120, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#interaction, http://sbolstandard.org/example/laci_inverter/LacI_pLacI
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4
- http://www.partsregistry.org/BBa_J61120, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://sbolstandard.org/example/toogleswicth, http://sbols.org/v2#language, http://identifiers.org/edam/format_2585
- http://www.partsregistry.org/BBa_J61130, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/BBa_J61130
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3, http://sbols.org/v2#displayId, anno3
- http://www.partsregistry.org/BBa_C0040, http://purl.org/dc/terms/title, tetR
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno2
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.partsregistry.org/BBa_J61130, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://sbolstandard.org/example/laci_inverter/TF, http://sbols.org/v2#definition, http://identifiers.org/uniprot/P03023
- http://www.partsregistry.org/ECK120029600, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.partsregistry.org/ECK120029600, http://sbols.org/v2#displayId, ECK120029600
- http://sbolstandard.org/example/toggle_switch/laci_inverter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Module
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130, http://sbols.org/v2#displayId, BBa_J61130
- http://www.partsregistry.org/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://identifiers.org/uniprot/P03023, http://sbols.org/v2#displayId, P03023
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://sbols.org/v2#local, http://sbolstandard.org/example/toggle_switch/TetR
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#MapsTo
- http://www.virtualparts.org/part/BBa_J61120, http://sbols.org/v2#elements, aaagacaggacc
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://sbols.org/v2#end, 742
- http://www.partsregistry.org/ECK120029600, http://sbols.org/v2#sequence, http://www.virtualparts.org/part/ECK120029600
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/anno2
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno5
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101, http://sbols.org/v2#displayId, BBa_J61101
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4
- http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping, http://sbols.org/v2#displayId, LacI_mapping
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.partsregistry.org/BBa_C0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5, http://sbols.org/v2#displayId, anno5
- http://identifiers.org/uniprot/P03023, http://sbols.org/v2#persistentIdentity, http://identifiers.org/uniprot/P03023
- http://sbolstandard.org/example/laci_inverter, http://sbols.org/v2#functionalComponent, http://sbolstandard.org/example/laci_inverter/TF
- http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno1, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1
- http://www.virtualparts.org/part/BBa_J61101, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/BBa_J61101
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2, http://sbols.org/v2#displayId, anno2
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno1
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno3/location3
- http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Participation
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno2
- http://www.virtualparts.org/part/BBa_C0040, http://sbols.org/v2#elements, atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://sbolstandard.org/example/laci_inverter/TF, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2
- http://sbolstandard.org/example/laci_inverter/promoter, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_R0010
- http://www.partsregistry.org/BBa_R0010, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/BBa_J61130, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023, http://sbols.org/v2#displayId, P03023
- http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600, http://sbols.org/v2#definition, http://www.partsregistry.org/ECK120029600
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://sbolstandard.org/example/tetr_inverter/promoter, http://sbols.org/v2#displayId, promoter
- http://www.partsregistry.org/BBa_E0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.partsregistry.org/ECK120029600, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.virtualparts.org/part/pIKERightCassette_1/anno6/location6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://identifiers.org/uniprot/Q6QR72, http://sbols.org/v2#persistentIdentity, http://identifiers.org/uniprot/Q6QR72
- http://www.partsregistry.org/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1, http://sbols.org/v2#location, http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1
- http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2, http://sbols.org/v2#component, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120
- http://www.partsregistry.org/BBa_R0010, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.virtualparts.org/part/pIKELeftCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKELeftCassette_1/anno1
- http://identifiers.org/uniprot/Q6QR72, http://purl.org/dc/terms/description, TetR protein
- http://www.partsregistry.org/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_C0012
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://sbols.org/v2#end, 1197
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/pIKERightCassette_1, http://sbols.org/v2#sequenceAnnotation, http://www.virtualparts.org/part/pIKERightCassette_1/anno1
- http://sbolstandard.org/example/toggle_switch/TetR, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/toggle_switch/TetR
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4
- http://sbolstandard.org/example/toggle_switch/TetR, http://sbols.org/v2#displayId, TetR
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010, http://sbols.org/v2#participant, http://sbolstandard.org/example/laci_inverter/promoter
- http://www.partsregistry.org/BBa_J61101, http://purl.org/dc/terms/title, BBa_J61101 RBS
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120
- http://identifiers.org/uniprot/P42212, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://sbolstandard.org/example/toogleswicth, http://sbols.org/v2#displayId, toogleswicth
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4, http://sbols.org/v2#start, 1198
- http://www.virtualparts.org/part/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.partsregistry.org/ECK120033736, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://sbolstandard.org/example/toggle_switch/LacI, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno3
- http://sbolstandard.org/example/tetr_inverter/promoter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#FunctionalComponent
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://sbols.org/v2#start, 730
- http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101, http://sbols.org/v2#definition, http://www.partsregistry.org/BBa_J61101
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1, http://sbols.org/v2#displayId, anno1
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno5/location5
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3
- http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.virtualparts.org/part/BBa_J61120, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKERightCassette_1/anno2/location2
- http://www.virtualparts.org/part/pIKERightCassette_1/anno1, http://sbols.org/v2#displayId, anno1
- http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023, http://sbols.org/v2#persistentIdentity, http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023
- http://www.virtualparts.org/part/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4/location4, http://sbols.org/v2#displayId, location4
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1, http://sbols.org/v2#displayId, location1
- http://www.virtualparts.org/part/pIKERightCassette_1/anno4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.virtualparts.org/part/pIKERightCassette_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://sbols.org/v2#start, 1286
- http://sbolstandard.org/example/tetr_inverter/promoter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.virtualparts.org/part/pIKELeftCassette_1/anno1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKELeftCassette_1/anno1
- http://www.partsregistry.org/BBa_E0040, http://purl.org/dc/terms/description, gfp coding sequence
- http://www.partsregistry.org/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.partsregistry.org/BBa_R0010
- http://www.virtualparts.org/part/pIKERightCassette_1/anno3, http://sbols.org/v2#displayId, anno3
- http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1, http://sbols.org/v2#persistentIdentity, http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1
- http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml:
- http://sbolstandard.org/example/toggle_switch, http://purl.org/dc/terms/created, 2003-12-04T12:00:00Z
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:17 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-REFINEMENT TYPE IS USEREMOTE
-REFINEMENT TYPE IS USEREMOTE
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:17 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 55,
- Property: components[7].subComponents[2].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 68,
- Property: components[3].subComponents[3].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[3].subComponents[1].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 56,
- Property: components[3].subComponents[3].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 729,
- Property: components[3].subComponents[5].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:54, Calculated location length:55, Sequence: http://www.virtualparts.org/part/BBa_R0040,
- Value: [http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040/location1],
- Property: components[7].subComponents[2].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:54, Calculated location length:55, Sequence: http://www.virtualparts.org/part/BBa_R0010,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010/location1],
- Property: components[3].subComponents[1].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1464,
- Property: components[3].subComponents[4].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736/location6,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:1128, Calculated location length:1129, Sequence: http://www.virtualparts.org/part/BBa_C0012,
- Value: [http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012/location3],
- Property: components[7].subComponents[1].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 68,
- Property: components[7].subComponents[3].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:90, Calculated location length:91, Sequence: http://www.virtualparts.org/part/ECK120029600,
- Value: [http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600/location4],
- Property: components[7].subComponents[0].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 55,
- Property: components[3].subComponents[1].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 743,
- Property: components[3].subComponents[2].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040/location5,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 69,
- Property: components[7].subComponents[1].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:12, Calculated location length:13, Sequence: http://www.virtualparts.org/part/BBa_J61101,
- Value: [http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101/location2],
- Property: components[7].subComponents[3].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:660, Calculated location length:661, Sequence: http://www.virtualparts.org/part/BBa_C0040,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040/location3],
- Property: components[3].subComponents[5].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1197,
- Property: components[7].subComponents[1].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1285,
- Property: components[11].subComponents[1].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[7].subComponents[2].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 730,
- Property: components[3].subComponents[0].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130/location4,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:90, Calculated location length:91, Sequence: http://www.virtualparts.org/part/ECK120033736,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736/location6],
- Property: components[3].subComponents[4].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:12, Calculated location length:13, Sequence: http://www.virtualparts.org/part/BBa_J61130,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130/location4],
- Property: components[3].subComponents[0].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 2834,
- Property: components[11].subComponents[0].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 56,
- Property: components[7].subComponents[3].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1288,
- Property: components[7].subComponents[0].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600/location4,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 69,
- Property: components[3].subComponents[5].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040/location3,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1286,
- Property: components[11].subComponents[0].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1/location2,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1198,
- Property: components[7].subComponents[0].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600/location4,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1554,
- Property: components[3].subComponents[4].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736/location6,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:720, Calculated location length:721, Sequence: http://www.virtualparts.org/part/BBa_E0040,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040/location5],
- Property: components[3].subComponents[2].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[11].subComponents[1].locations[0].start,
- Entity URI: http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1/location1,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 1463,
- Property: components[3].subComponents[2].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040/location5,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 742,
- Property: components[3].subComponents[0].locations[0].end,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130/location4,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:12, Calculated location length:13, Sequence: http://www.virtualparts.org/part/BBa_J61120,
- Value: [http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120/location2],
- Property: components[3].subComponents[3].hasLocation,
- Entity URI: http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-ComponentDefinition http://www.partsregistry.org/ECK120033736 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_C0040 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_J61101 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_J61120 not found in java32.xml
-ComponentDefinition http://www.virtualparts.org/part/pIKE_Toggle_1 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_R0010 not found in java32.xml
-ComponentDefinition http://identifiers.org/uniprot/P03023 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/ECK120029600 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_C0012 not found in java32.xml
-ComponentDefinition http://identifiers.org/uniprot/Q6QR72 not found in java32.xml
-ComponentDefinition http://www.virtualparts.org/part/pIKELeftCassette_1 not found in java32.xml
-ComponentDefinition http://identifiers.org/uniprot/P42212 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_R0040 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_E0040 not found in java32.xml
-ComponentDefinition http://www.virtualparts.org/part/pIKERightCassette_1 not found in java32.xml
-ComponentDefinition http://www.partsregistry.org/BBa_J61130 not found in java32.xml
-Sequence http://www.virtualparts.org/part/ECK120029600 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_E0040 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_C0012 not found in java32.xml
-Sequence http://www.virtualparts.org/part/ECK120033736 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_J61130 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_C0040 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_R0040 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_R0010 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_J61120 not found in java32.xml
-Sequence http://www.virtualparts.org/part/BBa_J61101 not found in java32.xml
-ModuleDefinition http://sbolstandard.org/example/laci_inverter not found in java32.xml
-ModuleDefinition http://sbolstandard.org/example/tetr_inverter differ.
-->FunctionalComponent http://sbolstandard.org/example/tetr_inverter/TF not found in java32.xml
-->FunctionalComponent http://sbolstandard.org/example/tetr_inverter/promoter not found in java32.xml
-->Interaction http://sbolstandard.org/example/tetr_inverter/LacI_pLacI differ.
---->Participation http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72 not found in java32.xml
---->Participation http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040 not found in java32.xml
-ModuleDefinition http://sbolstandard.org/example/toggle_switch differ.
-->FunctionalComponent http://sbolstandard.org/example/toggle_switch/TetR not found in java32.xml
-->FunctionalComponent http://sbolstandard.org/example/toggle_switch/LacI not found in java32.xml
-->Module http://sbolstandard.org/example/toggle_switch/tetr_inverter not found in java32.xml
-->Module http://sbolstandard.org/example/toggle_switch/laci_inverter not found in java32.xml
-Model http://sbolstandard.org/example/toogleswicth not found in java32.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
-Python Score = 7
-Java Score = 28
-Number of Files = 48
-File: /Users/myers/git/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml, not in python32.xml:
- http://www.async.ece.utah.edu/myPart1/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/myPart3/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/myPart2/1.0, http://sbols.org/v2#version, 1.0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml:
- http://www.async.ece.utah.edu/myPart3/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/myPart1/1.0, http://sbols.org/v2#version, 1
- http://www.async.ece.utah.edu/myPart2/1.0, http://sbols.org/v2#version, 1
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:20 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:21 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml
-Python Score = 7
-Java Score = 29
-Number of Files = 49
-File: /Users/myers/git/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml, not in python32.xml:
- http://www.async.ece.utah.edu/GenericTopLevel3/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/GenericTopLevel1/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericTopLevel1
- http://www.async.ece.utah.edu/GenericTopLevel1/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, urn:bbn.com:tasbe:grn/RegulatoryReaction1
- http://www.async.ece.utah.edu/GenericTopLevel2/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, urn:bbn.com:tasbe:grn/RegulatoryReaction2
- http://www.async.ece.utah.edu/GenericTopLevel3/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, urn:bbn.com:tasbe:grn/RegulatoryReaction3
- http://www.async.ece.utah.edu/GenericTopLevel1/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/GenericTopLevel1/1.0, http://sbols.org/v2#displayId, GenericTopLevel1
- http://www.async.ece.utah.edu/GenericTopLevel2/1.0, http://sbols.org/v2#displayId, GenericTopLevel2
- http://www.async.ece.utah.edu/GenericTopLevel2/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/GenericTopLevel3/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericTopLevel3
- http://www.async.ece.utah.edu/GenericTopLevel3/1.0, http://sbols.org/v2#displayId, GenericTopLevel3
- http://www.async.ece.utah.edu/GenericTopLevel2/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/GenericTopLevel2
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:23 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:23 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml
-Python Score = 7
-Java Score = 30
-Number of Files = 50
-File: /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Comparing original SBOL2 to converted SBOL2 using Python
-Python conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:26 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:26 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-10503 - The elements property of a Sequence MUST be consistent with its encoding property.,
- Value: ACGTURYSWKMBDHVN-.,
- Property: sequences[0].elements,
- Entity URI: http://www.async.ece.utah.edu/1.0/pLactetRSeq,
- Entity Type: class org.sbolstandard.core3.entity.Sequence
-
-sbol3-10503 - The elements property of a Sequence MUST be consistent with its encoding property.,
- Value: ACGTURYSWKMBDHVN-.,
- Property: sequences[1].elements,
- Entity URI: http://www.async.ece.utah.edu/1.0/pLacSeq,
- Entity Type: class org.sbolstandard.core3.entity.Sequence
-
-sbol3-10503 - The elements property of a Sequence MUST be consistent with its encoding property.,
- Value: ACGTURYSWKMBDHVN-.,
- Property: sequences[2].elements,
- Entity URI: http://www.async.ece.utah.edu/1.0/tetRSeq,
- Entity Type: class org.sbolstandard.core3.entity.Sequence
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Sequence http://www.async.ece.utah.edu/pLacSeq/1.0 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/pLactetRSeq/1.0 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/tetRSeq/1.0 not found in java32.xml
-GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel1/1.0 not found in multipleSequences.xml
-GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel3/1.0 not found in multipleSequences.xml
-GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel2/1.0 not found in multipleSequences.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
-Python Score = 8
-Java Score = 30
-Number of Files = 51
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1467.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1467.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation3
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation0/range
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/genBankConversion#label, His tag with EK cleavage site
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://sbols.org/v2#end, 2333
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation5/range
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation0
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation7/range
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation6/range
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation4
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation2/range
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://sbols.org/v2#start, 2334
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation5/range
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#displayId, pAGM1467
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation4
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM1467_seq
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation1
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation6/range
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/genBankConversion#label, AATG 4 bp overhang
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation0/range
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation4/range
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://purl.org/dc/terms/title, AATG 4 bp overhang
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation4/range
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation3/range
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation6
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation2
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation3/range
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation5
- http://www.async.ece.utah.edu/pAGM1467_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/genBankConversion#featureType, N-Region
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation2/range
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://sbols.org/v2#end, 2386
- http://www.async.ece.utah.edu/pAGM1467/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation0
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation1/range
- http://www.async.ece.utah.edu/pAGM1467, http://www.ncbi.nlm.nih.gov/genbank#date, 7-NOV-2012
- http://www.async.ece.utah.edu/pAGM1467, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM1467
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://purl.org/dc/terms/title, omega TMV (w.t.)
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation2
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1467_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1467/annotation7/range
- http://www.async.ece.utah.edu/pAGM1467/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM1467, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation6
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/genBankConversion#label, omega TMV (w.t.)
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation1
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM1467/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation7
- http://www.async.ece.utah.edu/pAGM1467/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation1/range
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM1467, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM1467/annotation7, http://purl.org/dc/terms/title, His tag with EK cleavage site
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1467/annotation7
- http://www.async.ece.utah.edu/pAGM1467_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467_seq
- http://www.async.ece.utah.edu/pAGM1467_seq, http://sbols.org/v2#displayId, pAGM1467_seq
- http://www.async.ece.utah.edu/pAGM1467/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM1467/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM1467/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM1467/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1467/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM1467_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATACATGGGCAGCAGCCACCACCACCACCACCACAGCAGCGGCGACGACGACGACAA
- http://www.async.ece.utah.edu/pAGM1467/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation5
- http://www.async.ece.utah.edu/pAGM1467/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1467/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1467/annotation3
- http://www.async.ece.utah.edu/pAGM1467, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1467.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1467.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:28 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:29 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1467.xml
-Python Score = 8
-Java Score = 31
-Number of Files = 52
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1479.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1479.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation1/range
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation7/range
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation6
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation5/range
- http://www.async.ece.utah.edu/pAGM1479, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation3/range
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation4/range
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/genBankConversion#label, omega (TMV)
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation0/range
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#displayId, pAGM1479
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation1/range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation1
- http://www.async.ece.utah.edu/pAGM1479_seq, http://sbols.org/v2#displayId, pAGM1479_seq
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation5/range
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM1479, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation6/range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation5
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation5
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation7/range
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://sbols.org/v2#end, 2333
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM1479_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM1479, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation4
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation2
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://sbols.org/v2#end, 2365
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://purl.org/dc/terms/title, 6X His
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1479_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479_seq
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation3
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation2/range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation2
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM1479/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM1479, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM1479, http://www.ncbi.nlm.nih.gov/genbank#date, 4-FEB-2013
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1479_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATACATGGGCAGCCACCACCACCACCACCACAGCGG
- http://www.async.ece.utah.edu/pAGM1479/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM1479, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM1479
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation1
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation0
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://sbols.org/v2#start, 2334
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation7
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation0/range
- http://www.async.ece.utah.edu/pAGM1479/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation2/range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1479/annotation3
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://purl.org/dc/terms/title, omega (TMV)
- http://www.async.ece.utah.edu/pAGM1479/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM1479/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation4/range
- http://www.async.ece.utah.edu/pAGM1479, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM1479_seq
- http://www.async.ece.utah.edu/pAGM1479/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation7
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation6/range
- http://www.async.ece.utah.edu/pAGM1479/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1479/annotation3/range
- http://www.async.ece.utah.edu/pAGM1479/annotation7, http://sbols.org/genBankConversion#label, 6X His
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation4
- http://www.async.ece.utah.edu/pAGM1479/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM1479/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1479/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation0
- http://www.async.ece.utah.edu/pAGM1479/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM1479/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1479/annotation6
- http://www.async.ece.utah.edu/pAGM1479/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1479.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1479.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:31 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1479.xml
-Python Score = 8
-Java Score = 32
-Number of Files = 53
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1482.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1482.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/genBankConversion#position, position0
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1482_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATAACATGTTGTCACTACGTCAATCTATAAGATTTTTCAAGCCAGCCACAAGAACTTTGTGTAGCTCTCGTTATCTGCTGCAGCAAAAACC
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation2/range
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation3
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation4
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation2/range
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation6
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation2
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation0/range1
- http://www.async.ece.utah.edu/pAGM1482, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/genBankConversion#label, CoxIV mitochondrial target peptide (S. ceravisae)
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation2
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation4
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/v2#end, 1
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation4/range
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation5
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM1482_seq, http://sbols.org/v2#displayId, pAGM1482_seq
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM1482_seq
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation0
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482_seq
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation6/range
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation6/range
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://sbols.org/v2#end, 2334
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/genBankConversion#multiRangeType, join
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/v2#displayId, range1
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation0/range1
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation5/range
- http://www.async.ece.utah.edu/pAGM1482/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation1/range
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation5
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM1482, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://purl.org/dc/terms/title, omega (TMV)
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/v2#displayId, range0
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pAGM1482, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM1482
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation1/range
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation3
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/genBankConversion#label, omega (TMV)
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation0
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation1
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation3/range
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/v2#end, 2420
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation0/range0
- http://www.async.ece.utah.edu/pAGM1482, http://www.ncbi.nlm.nih.gov/genbank#date, 7-NOV-2012
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#displayId, pAGM1482
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://purl.org/dc/terms/title, CoxIV mitochondrial target peptide (S. ceravisae)
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation1
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM1482/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM1482/annotation0/range0
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range1, http://sbols.org/genBankConversion#position, position1
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM1482/annotation0/range0, http://sbols.org/v2#start, 2335
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM1482, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM1482/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation5/range
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM1482/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM1482_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM1482/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM1482/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM1482/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation4/range
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM1482/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM1482, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM1482/annotation6
- http://www.async.ece.utah.edu/pAGM1482/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM1482/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM1482_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM1482/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM1482/annotation3/range
- http://www.async.ece.utah.edu/pAGM1482/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1482.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1482.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:34 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:35 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM1482.xml
-Python Score = 8
-Java Score = 33
-Number of Files = 54
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5331.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5331.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM5331, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation4
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation4/range
- http://www.async.ece.utah.edu/pAGM5331_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation2/range
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://purl.org/dc/terms/title, omega (TMV)
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation5
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation5
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation1
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM5331_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation7
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM5331_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331_seq
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://purl.org/dc/terms/title, AATG
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation2
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation6/range
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation7/range
- http://www.async.ece.utah.edu/pAGM5331, http://www.ncbi.nlm.nih.gov/genbank#date, 26-FEB-2013
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation4
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation2/range
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation3/range
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation0
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation0/range
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation0/range
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pAGM5331_seq, http://sbols.org/v2#displayId, pAGM5331_seq
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://sbols.org/v2#end, 2377
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation3/range
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation1
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation2
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation6
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM5331_seq
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation1/range
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://purl.org/dc/terms/title, nuclear localisation signsal (SV40)
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://sbols.org/v2#start, 2334
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/genBankConversion#featureType, Transit_peptide
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation0
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation6/range
- http://www.async.ece.utah.edu/pAGM5331, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation3
- http://www.async.ece.utah.edu/pAGM5331/annotation0, http://sbols.org/genBankConversion#label, AATG
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/genBankConversion#label, omega (TMV)
- http://www.async.ece.utah.edu/pAGM5331_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATACATGGCTTCTAGCCCACCGAAGAAGAAGCGGAAGGTCAGCTGGAA
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM5331/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#displayId, pAGM5331
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://sbols.org/v2#end, 2333
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/genBankConversion#label, nuclear localisation signsal (SV40)
- http://www.async.ece.utah.edu/pAGM5331, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM5331
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation6
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331
- http://www.async.ece.utah.edu/pAGM5331/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation4/range
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation1/range
- http://www.async.ece.utah.edu/pAGM5331/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation7/range
- http://www.async.ece.utah.edu/pAGM5331/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM5331/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5331/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM5331/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM5331/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation5/range
- http://www.async.ece.utah.edu/pAGM5331/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM5331/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5331/annotation5/range
- http://www.async.ece.utah.edu/pAGM5331/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5331/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5331/annotation3
- http://www.async.ece.utah.edu/pAGM5331, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5331/annotation7
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5331.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5331.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:37 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:37 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5331.xml
-Python Score = 8
-Java Score = 34
-Number of Files = 55
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5343.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5343.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation5/range
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation1
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation6
- http://www.async.ece.utah.edu/pAGM5343_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://purl.org/dc/terms/title, TMV omega
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation2
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM5343_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343_seq
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation8
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/genBankConversion#featureType, Transit_peptide
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation7
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation3/range
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation0/range
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://sbols.org/v2#end, 2441
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM5343_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation8/range
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://sbols.org/v2#start, 2335
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM5343_seq
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation4/range
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation1/range
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation0
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation3
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation3/range
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation0
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation6
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation2
- http://www.async.ece.utah.edu/pAGM5343, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM5343
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATAACATGGGGAAGCAAATGGCCGCCCTGTGTGGCTTTCTCCTCGTGGCGTTGCTCTGGCTCACGCCCGACGTCGCGTCAGCAGGCAGCCACCACCACCACCACCACAGCGG
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation7/range
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation2/range
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/genBankConversion#label, rice apoplast targeting signal
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/genBankConversion#vntifkey, 95
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://sbols.org/v2#end, 2334
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation5
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation4/range
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation8
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM5343, http://www.ncbi.nlm.nih.gov/genbank#date, 26-FEB-2013
- http://www.async.ece.utah.edu/pAGM5343/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation0/range
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation3
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation4
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/v2#displayId, annotation8
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://sbols.org/genBankConversion#label, AATG 4 bp overhang
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation5/range
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://sbols.org/genBankConversion#label, HIS tag
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/genBankConversion#label, TMV omega
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation7/range, http://sbols.org/v2#end, 2412
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation7
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM5343/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation6/range
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation6/range
- http://www.async.ece.utah.edu/pAGM5343/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation1/range
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM5343, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://purl.org/dc/terms/title, rice apoplast targeting signal
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://sbols.org/v2#start, 2413
- http://www.async.ece.utah.edu/pAGM5343/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM5343/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation4
- http://www.async.ece.utah.edu/pAGM5343/annotation8/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation8/range
- http://www.async.ece.utah.edu/pAGM5343/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM5343_seq, http://sbols.org/v2#displayId, pAGM5343_seq
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation2/range
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#displayId, pAGM5343
- http://www.async.ece.utah.edu/pAGM5343, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5343/annotation1
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM5343/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5343/annotation7/range
- http://www.async.ece.utah.edu/pAGM5343/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM5343/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5343/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation0, http://purl.org/dc/terms/title, AATG 4 bp overhang
- http://www.async.ece.utah.edu/pAGM5343/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM5343, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM5343, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM5343/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM5343/annotation8, http://purl.org/dc/terms/title, HIS tag
- http://www.async.ece.utah.edu/pAGM5343/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5343/annotation5
- http://www.async.ece.utah.edu/pAGM5343/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5343.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5343.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:40 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:40 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5343.xml
-Python Score = 8
-Java Score = 35
-Number of Files = 56
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5355.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5355.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://sbols.org/v2#end, 2334
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation6
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation2
- http://www.async.ece.utah.edu/pAGM5355_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355_seq
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pAGM5355_seq, http://sbols.org/v2#displayId, pAGM5355_seq
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation4
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5355, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/genBankConversion#label, RbcS chloroplast transit peptide (synthetic)
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation0/range0
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pAGM5355_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation2/range
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/v2#end, 2540
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/genBankConversion#featureType, Transit_peptide
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/v2#end, 1
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://sbols.org/v2#end, 2511
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/genBankConversion#multiRangeType, join
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/genBankConversion#label, 6xHis
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation5/range
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation6
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation6/range
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation5
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation2/range
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/v2#displayId, range1
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/genBankConversion#label, TMV omega
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation4/range
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation3/range
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation0
- http://www.async.ece.utah.edu/pAGM5355, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pAGM5355_seq
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation0
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://purl.org/dc/terms/title, 6xHis
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation4
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation5
- http://www.async.ece.utah.edu/pAGM5355, http://www.ncbi.nlm.nih.gov/genbank#date, 8-MAY-2013
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://sbols.org/v2#start, 2335
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://purl.org/dc/terms/title, RbcS chloroplast transit peptide (synthetic)
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation3/range
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://purl.org/dc/terms/title, TMV omega
- http://www.async.ece.utah.edu/pAGM5355, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5355_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATAAGAGCTCATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACATTTACAATTATCGATAACATGGCTTCTTCTATGCTTTCTTCTGCTGCTGTTGTTGCTACTCGTGCTAGTGCTGCTCAAGCTAGTATGGTTGCTCCTTTTACTGGACTTAAGTCTGCTGCTTCTTTTCCTGTTACTAGAAAGCAAAACAACCTTGATATTACTTCTATTGCTAGTAACGGAGGAAGAGTTCGAGCAGGCAGCCACCACCACCACCACCACAGCGG
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#displayId, pAGM5355
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation1
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/genBankConversion#position, position1
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation5/range
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/v2#start, 2512
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/genBankConversion#position, position0
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355, http://www.ncbi.nlm.nih.gov/genbank#locus, pAGM5355
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pAGM5355/annotation5/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pAGM5355_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation0/range0
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://sbols.org/v2#displayId, range0
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation0/range1
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation1/range
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation1
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation3
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pAGM5355/annotation2
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pAGM5355/annotation1/range
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://sbols.org/genBankConversion#vntifkey, 95
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation4/range
- http://www.async.ece.utah.edu/pAGM5355, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pAGM5355/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pAGM5355/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pAGM5355/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pAGM5355/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation6/range
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pAGM5355/annotation0/range1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation0/range1
- http://www.async.ece.utah.edu/pAGM5355/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pAGM5355/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pAGM5355/annotation3
- http://www.async.ece.utah.edu/pAGM5355/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pAGM5355/annotation2, http://sbols.org/v2#displayId, annotation2
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5355.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5355.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:43 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:43 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGM5355.xml
-Python Score = 8
-Java Score = 36
-Number of Files = 57
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pAGT707.xmlk
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-2025-10-21T18:19:45.560Z:WARNING:file:///Users/myers/git/SBOLTestSuite/SBOL2/?xml version="1.0" ? does not look like a valid URI, trying to serialize this will break.
-2025-10-21T18:19:45.560Z:WARNING:rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:gbConv="http://sbols.org/genBankConversion#" xmlns:sbol="http://sbols.org/v2#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:genbank="http://www.ncbi.nlm.nih.gov/genbank#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" does not look like a valid URI, trying to serialize this will break.
-2025-10-21T18:19:45.560Z:WARNING:sbol:ComponentDefinition rdf:about="http://www.async.ece.utah.edu/Exported_File" does not look like a valid URI, trying to serialize this will break.
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/graph.py", line 1494, in parse
- parser.parse(source, self, **args)
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 2021, in parse
- p.loadStream(stream)
- ~~~~~~~~~~~~^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 479, in loadStream
- return self.loadBuf(stream.read()) # Not ideal
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 485, in loadBuf
- self.feed(buf)
- ~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 511, in feed
- i = self.directiveOrStatement(s, j)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 532, in directiveOrStatement
- return self.checkDot(argstr, j)
- ~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 1214, in checkDot
- self.BadSyntax(argstr, j, "expected '.' or '}' or ']' at end of statement")
- ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/plugins/parsers/notation3.py", line 1730, in BadSyntax
- raise BadSyntax(self._thisDoc, self.lines, argstr, i, msg)
-rdflib.plugins.parsers.notation3.BadSyntax:
-
-During handling of the above exception, another exception occurred:
-
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-diff", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 235, in main
- return file_diff(args.file1, args.file2, silent=args.silent,
- strip_backport_properties=args.strip_backport_properties)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 185, in file_diff
- return _diff_rdf(fpath1, _load_rdf(fpath1), fpath2, _load_rdf(fpath2), silent=silent,
- ~~~~~~~~~^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol_diff.py", line 25, in _load_rdf
- graph1.parse(fpath, format=rdf_format)
- ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/rdflib/graph.py", line 1497, in parse
- raise ParserError(
- ...<3 lines>...
- )
-rdflib.exceptions.ParserError: Could not guess RDF format for <_io.BufferedReader name='/Users/myers/git/SBOLTestSuite/SBOL2/pAGT707.xmlk'> from file extension so tried Turtle but failed.You can explicitly specify format using the format argument.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pAGT707.xmlk
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:46 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:47 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pAGT707.xmlk
-Python Score = 8
-Java Score = 37
-Number of Files = 58
-File: /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/partseq_153, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/partseq_187, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_187
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0012
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator
- http://www.async.ece.utah.edu/BBa_R0040, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_R0040
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2, http://sbols.org/v2#displayId, Repressor2
- http://www.async.ece.utah.edu/BBa_R0040, http://purl.org/dc/terms/description, TetR repressible promoter
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:2bc8890b-9fc3-44e8-9606-6b5e7dd7a690
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#displayId, RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/BBa_C0012, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_C0012
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://sbols.org/v2#displayId, Repressor2_annotation
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0012
- http://www.async.ece.utah.edu/BBa_C0012, http://purl.org/dc/terms/description, lacI repressor from E. coli (+LVA)
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor2, http://www.w3.org/ns/prov#wasDerivedFrom, urn:2c324e1d-484e-4597-b92c-657b82eb8483
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/ns/prov#wasDerivedFrom, urn:49f0ad6c-dec4-4b82-a989-d9ce22ac8c58
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/partseq_187, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKELeftCasette, http://purl.org/dc/terms/title, pIKE Left Casette
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Repressor2
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://sbols.org/v2#displayId, BBa_R0040_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_R0040, http://purl.org/dc/terms/title, p(tetR)
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:dd9e467e-eb95-4bda-8788-c13a08e745c9
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#displayId, Repressor2
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:3408ce9e-135e-4fb3-ba0f-42f8eb43dd33
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://sbols.org/v2#displayId, BBa_R0040_cons_Repressor2
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_187
- http://www.async.ece.utah.edu/Repressor2/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#displayId, BBa_C0012_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:678f5ee4-ef38-4c8e-a235-145a459b2128
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:14dfcbba-9c70-43de-8e14-b3d7c5d88ee7
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/partseq_187, http://sbols.org/v2#displayId, partseq_187
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/partseq_187, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_187
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/ns/prov#wasDerivedFrom, urn:7376e955-1f10-411b-b123-ac37410d81f2
- http://www.async.ece.utah.edu/partseq_187, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_153
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor2/RBS_annotation
- http://www.async.ece.utah.edu/partseq_187, http://sbols.org/v2#elements, tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac
- http://www.async.ece.utah.edu/BBa_R0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKELeftCasette, http://www.w3.org/ns/prov#wasDerivedFrom, urn:f71298e4-a79b-4f94-ae8a-22b1f6d11d8b
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://sbols.org/v2#displayId, Repressor2_cons_Terminator
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://sbols.org/v2#end, 54
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator
- http://www.async.ece.utah.edu/partseq_153, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_153
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#displayId, pIKELeftCasette
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_153
- http://www.async.ece.utah.edu/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#elements, atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#displayId, RBS_annotation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pIKELeftCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_R0040
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator_annotation, http://sbols.org/v2#displayId, Terminator_annotation
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKELeftCasette/Terminator
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/pIKELeftCasette/Terminator, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#displayId, partseq_153
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_annotation
- http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2
- http://www.async.ece.utah.edu/BBa_C0012, http://purl.org/dc/terms/title, lacI
- http://www.async.ece.utah.edu/BBa_R0040, http://sbols.org/v2#displayId, BBa_R0040
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 54,
- Property: components[4].subComponents[1].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, 54], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040/range],
- Property: components[4].constraints[1].subject[http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040_cons_Repressor2,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Repressor2/RBS/genericLocation],
- Property: components[2].constraints[0].subject[http://www.async.ece.utah.edu/Repressor2/RBS].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[4].subComponents[1].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/pIKELeftCasette/BBa_R0040/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2/genericLocation],
- Property: components[4].constraints[0].subject[http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKELeftCasette/Repressor2_cons_Terminator,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:1128, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_153,
- Value: [http://www.async.ece.utah.edu/Repressor2/BBa_C0012/genericLocation],
- Property: components[2].subComponents[0].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor2/BBa_C0012,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Namespace {http://sbols.org/genBankConversion#} not found in partial_pIKE_left_cassette.xml
-Namespace {http://www.ncbi.nlm.nih.gov/genbank#} not found in partial_pIKE_left_cassette.xml
-ComponentDefinition http://www.async.ece.utah.edu/RBS not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0012 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Terminator not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/pIKELeftCasette not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_R0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Repressor2 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Exported_File not found in partial_pIKE_left_cassette.xml
-Sequence http://www.async.ece.utah.edu/partseq_153 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_187 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/Exported_File_seq not found in partial_pIKE_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
-Python Score = 8
-Java Score = 37
-Number of Files = 59
-File: /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml, not in python32.xml:
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#displayId, Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#elements, atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_E0040
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:3aec1249-b602-47e1-b919-8826ee71d6be
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#displayId, BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette, http://purl.org/dc/terms/title, pIKE Right Casette
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/description, promoter (lacI regulated)
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#displayId, Reporter_cons_Terminator
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:139fd881-e36b-4b19-acbe-6ed372f18676
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/ns/prov#wasDerivedFrom, urn:c951c2cc-8caa-46eb-9439-4680574ee169
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#displayId, RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_C0040, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#elements, caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacaca
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#displayId, rbsB_annotation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#displayId, Reporter_annotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/BBa_C0040, http://purl.org/dc/terms/description, tetracycline repressor from transposon Tn10 (+LVA)
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette, http://www.w3.org/ns/prov#wasDerivedFrom, urn:da0805ac-06ea-4de8-98dc-fc731d9c37a8
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/title, GFP
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#displayId, BBa_R0010_annotation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d1e2df30-12bf-499a-85d2-95736ec9a183
- http://www.async.ece.utah.edu/partseq_5309, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_5309
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:dd88ec76-734a-40eb-8594-a4e26aa7b595
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0040
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#displayId, partseq_5309
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/Repressor1/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/ns/prov#wasDerivedFrom, urn:22544a89-264a-4b59-b7a7-8137b262bbc2
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_R0010
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0040
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_5309
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#displayId, rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_C0040, http://purl.org/dc/terms/title, tetR
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/title, LacI
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#displayId, Terminator_annotation
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#displayId, partseq_154
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:f864600d-52c9-459f-bc49-4b4133695b01
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Reporter/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:663cb06c-ae84-4eb6-aca1-bd7c83ed32cb
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:5596babc-99de-478a-964d-425f14926186
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/partseq_154, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#displayId, BBa_E0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d544b3f6-0a37-45ac-83a9-5b7a6b0b19bd
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#displayId, partseq_185
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/ns/prov#wasDerivedFrom, urn:3b787f85-3d90-4519-a124-d0041b7da66b
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:f6071601-1d80-4bd1-9142-21cd931cc545
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#displayId, pIKERightCasette
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#elements, atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#displayId, RBS_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#displayId, Repressor1_annotation
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/partseq_5309, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_154
- http://www.async.ece.utah.edu/partseq_154, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_154
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/description, green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP (SwissProt: P42212
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000104
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_154
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_5309
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/ns/prov#wasDerivedFrom, urn:a8ebdf89-b8ad-48d5-a7e2-6cba33225e17
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#end, 200
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#displayId, BBa_C0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_185
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:52 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:52 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:660, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_154,
- Value: [http://www.async.ece.utah.edu/Repressor1/BBa_C0040/genericLocation],
- Property: components[1].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/BBa_C0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:720, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_5309,
- Value: [http://www.async.ece.utah.edu/Reporter/BBa_E0040/genericLocation],
- Property: components[4].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, 200], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range],
- Property: components[8].constraints[1].subject[http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[8].subComponents[2].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Repressor1/RBS/genericLocation],
- Property: components[1].constraints[0].subject[http://www.async.ece.utah.edu/Repressor1/RBS].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/Reporter/genericLocation],
- Property: components[8].constraints[2].subject[http://www.async.ece.utah.edu/pIKERightCasette/Reporter].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 200,
- Property: components[8].subComponents[2].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Reporter/rbsB/genericLocation],
- Property: components[4].constraints[0].subject[http://www.async.ece.utah.edu/Reporter/rbsB].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/Repressor1/genericLocation],
- Property: components[8].constraints[0].subject[http://www.async.ece.utah.edu/pIKERightCasette/Repressor1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Namespace {http://sbols.org/genBankConversion#} not found in partial_pIKE_right_casette.xml
-Namespace {http://www.ncbi.nlm.nih.gov/genbank#} not found in partial_pIKE_right_casette.xml
-ComponentDefinition http://www.async.ece.utah.edu/RBS not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Terminator not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/pIKERightCasette not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Reporter not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Repressor1 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_R0010 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_E0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/rbsB not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Exported_File not found in partial_pIKE_right_casette.xml
-Sequence http://www.async.ece.utah.edu/partseq_154 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_5309 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_185 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/Exported_File_seq not found in partial_pIKE_right_casette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
-Python Score = 8
-Java Score = 37
-Number of Files = 60
-File: /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml, not in python32.xml:
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/title, LacI
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_C0040, http://purl.org/dc/terms/title, tetR
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:f6071601-1d80-4bd1-9142-21cd931cc545
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/description, green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP (SwissProt: P42212
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#displayId, RBS_annotation
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#elements, atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa
- http://www.async.ece.utah.edu/partseq_5309, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/description, promoter (lacI regulated)
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#displayId, partseq_154
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/partseq_154, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:dd88ec76-734a-40eb-8594-a4e26aa7b595
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#displayId, partseq_185
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette, http://www.w3.org/ns/prov#wasDerivedFrom, urn:da0805ac-06ea-4de8-98dc-fc731d9c37a8
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#displayId, BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#displayId, Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0040
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/ns/prov#wasDerivedFrom, urn:22544a89-264a-4b59-b7a7-8137b262bbc2
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#displayId, rbsB_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d544b3f6-0a37-45ac-83a9-5b7a6b0b19bd
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#displayId, rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_5309
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_C0040, http://purl.org/dc/terms/description, tetracycline repressor from transposon Tn10 (+LVA)
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#displayId, BBa_R0010_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#displayId, Terminator_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#elements, atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#displayId, BBa_C0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:f864600d-52c9-459f-bc49-4b4133695b01
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#displayId, RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/partseq_154, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_154
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Reporter
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:3aec1249-b602-47e1-b919-8826ee71d6be
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:139fd881-e36b-4b19-acbe-6ed372f18676
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#displayId, pIKERightCasette
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/ns/prov#wasDerivedFrom, urn:3b787f85-3d90-4519-a124-d0041b7da66b
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#displayId, BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/partseq_5309, http://sbols.org/v2#displayId, partseq_5309
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/ns/prov#wasDerivedFrom, urn:a8ebdf89-b8ad-48d5-a7e2-6cba33225e17
- http://www.async.ece.utah.edu/partseq_154, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_154
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#displayId, Reporter_annotation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/partseq_5309, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_5309
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:663cb06c-ae84-4eb6-aca1-bd7c83ed32cb
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#end, 200
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_C0040, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette, http://purl.org/dc/terms/title, pIKE Right Casette
- http://www.async.ece.utah.edu/Reporter/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#displayId, Repressor1_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_5309
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#displayId, BBa_E0040_annotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000104
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#elements, caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacaca
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/pIKERightCasette, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/title, GFP
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_154
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:5596babc-99de-478a-964d-425f14926186
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_185
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/BBa_C0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Repressor1
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pIKERightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/pIKERightCasette/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator, http://sbols.org/v2#displayId, Reporter_cons_Terminator
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0040
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/Repressor1/BBa_C0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d1e2df30-12bf-499a-85d2-95736ec9a183
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/ns/prov#wasDerivedFrom, urn:c951c2cc-8caa-46eb-9439-4680574ee169
- http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pIKERightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pIKERightCasette/Terminator
- http://www.async.ece.utah.edu/BBa_C0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:54 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:55 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[8].subComponents[2].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Reporter/rbsB/genericLocation],
- Property: components[4].constraints[0].subject[http://www.async.ece.utah.edu/Reporter/rbsB].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/Reporter/genericLocation],
- Property: components[8].constraints[2].subject[http://www.async.ece.utah.edu/pIKERightCasette/Reporter].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/Reporter_cons_Terminator,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 200,
- Property: components[8].subComponents[2].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:660, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_154,
- Value: [http://www.async.ece.utah.edu/Repressor1/BBa_C0040/genericLocation],
- Property: components[1].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/BBa_C0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/Repressor1/genericLocation],
- Property: components[8].constraints[0].subject[http://www.async.ece.utah.edu/pIKERightCasette/Repressor1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/Repressor1_cons_Reporter,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Repressor1/RBS/genericLocation],
- Property: components[1].constraints[0].subject[http://www.async.ece.utah.edu/Repressor1/RBS].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0040,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:720, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_5309,
- Value: [http://www.async.ece.utah.edu/Reporter/BBa_E0040/genericLocation],
- Property: components[4].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, 200], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010/range],
- Property: components[8].constraints[1].subject[http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pIKERightCasette/BBa_R0010_cons_Repressor1,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Namespace {http://sbols.org/genBankConversion#} not found in partial_pIKE_right_cassette.xml
-Namespace {http://www.ncbi.nlm.nih.gov/genbank#} not found in partial_pIKE_right_cassette.xml
-ComponentDefinition http://www.async.ece.utah.edu/RBS not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Terminator not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/pIKERightCasette not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Reporter not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Repressor1 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_R0010 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_E0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/rbsB not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Exported_File not found in partial_pIKE_right_cassette.xml
-Sequence http://www.async.ece.utah.edu/partseq_154 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_5309 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_185 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/Exported_File_seq not found in partial_pIKE_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
-Python Score = 8
-Java Score = 37
-Number of Files = 61
-File: /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#displayId, pTAKLeftCassete
- http://www.async.ece.utah.edu/BBa_C0012, http://purl.org/dc/terms/title, lacI
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_C0012, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#displayId, RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/partseq_153, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_153
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#displayId, Repressor2
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://purl.org/dc/terms/title, pTAK Left Cassete
- http://www.async.ece.utah.edu/partseq_12077, http://sbols.org/v2#displayId, partseq_12077
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:53de82c6-ecf9-4899-8e06-0179ab03a9a0
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor2/RBS_annotation
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2, http://sbols.org/v2#displayId, Repressor2
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#displayId, partseq_153
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_153
- http://www.async.ece.utah.edu/partseq_153, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/BBa_C0012, http://purl.org/dc/terms/description, lacI repressor from E. coli (+LVA)
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_153
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#displayId, RBS_annotation
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://sbols.org/v2#displayId, Repressor2_cons_Terminator
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#displayId, BBa_K121014
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2
- http://www.async.ece.utah.edu/BBa_K121014, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_K121014
- http://www.async.ece.utah.edu/Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:032c2f83-39a5-44ee-a9cb-9b7be51d52ec
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:ecb1d4c8-653c-4c03-b647-71c839bb28e7
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://sbols.org/v2#displayId, Repressor2_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://sbols.org/v2#displayId, BBa_K121014_cons_Repressor2
- http://www.async.ece.utah.edu/BBa_K121014, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/partseq_12077, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014, http://sbols.org/v2#displayId, BBa_K121014
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_12077
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/ns/prov#wasDerivedFrom, urn:bcb44a78-ed3e-485b-b4a4-ec5cff683588
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://sbols.org/v2#displayId, Terminator_annotation
- http://www.async.ece.utah.edu/partseq_153, http://sbols.org/v2#elements, atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.async.ece.utah.edu/BBa_K121014, http://purl.org/dc/terms/description, promoter (lambda cI regulated)
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/partseq_12077, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_12077
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Repressor2
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_K121014
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation
- http://www.async.ece.utah.edu/Repressor2, http://www.w3.org/ns/prov#wasDerivedFrom, urn:6d179ea6-dcff-4da5-be76-4d343cb99e90
- http://www.async.ece.utah.edu/Repressor2/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/BBa_K121014, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_K121014
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://sbols.org/v2#displayId, BBa_K121014_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS
- http://www.async.ece.utah.edu/partseq_12077, http://sbols.org/v2#elements, gcatgcacagataaccatctgcggtgataaattatctctggcggtgttgacataaataccactggcggttataatgagcacatcagcagg
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:8c0016f6-eaef-4290-a4d6-761bdd3da3d8
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/ns/prov#wasDerivedFrom, urn:c26b0115-3c37-4aa7-9e98-c491b3db9a53
- http://www.async.ece.utah.edu/Repressor2/RBS, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor2/RBS_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation/range, http://sbols.org/v2#end, 90
- http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014
- http://www.async.ece.utah.edu/Repressor2, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor2/BBa_C0012
- http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2
- http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pTAKLeftCassete, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d0f2ca7b-33d4-4106-8b7a-4bfe7efa1a16
- http://www.async.ece.utah.edu/partseq_12077, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_C0012, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/partseq_12077, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_12077
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:c73c9f89-a174-43fc-9aa9-d250b3de02aa
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012, http://sbols.org/v2#displayId, BBa_C0012
- http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKLeftCassete/Terminator
- http://www.async.ece.utah.edu/Repressor2/BBa_C0012_annotation, http://sbols.org/v2#displayId, BBa_C0012_annotation
- http://www.async.ece.utah.edu/BBa_C0012, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:57 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:19:58 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2/genericLocation],
- Property: components[5].constraints[1].subject[http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pTAKLeftCassete/Repressor2_cons_Terminator,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 90,
- Property: components[5].subComponents[2].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[5].subComponents[2].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, 90], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014/range],
- Property: components[5].constraints[0].subject[http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pTAKLeftCassete/BBa_K121014_cons_Repressor2,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:1128, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_153,
- Value: [http://www.async.ece.utah.edu/Repressor2/BBa_C0012/genericLocation],
- Property: components[3].subComponents[0].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor2/BBa_C0012,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Repressor2/RBS/genericLocation],
- Property: components[3].constraints[0].subject[http://www.async.ece.utah.edu/Repressor2/RBS].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor2/RBS_cons_BBa_C0012,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Namespace {http://sbols.org/genBankConversion#} not found in partial_pTAK_left_cassette.xml
-Namespace {http://www.ncbi.nlm.nih.gov/genbank#} not found in partial_pTAK_left_cassette.xml
-ComponentDefinition http://www.async.ece.utah.edu/RBS not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0012 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Terminator not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_K121014 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Repressor2 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/pTAKLeftCassete not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Exported_File not found in partial_pTAK_left_cassette.xml
-Sequence http://www.async.ece.utah.edu/partseq_153 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_12077 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/Exported_File_seq not found in partial_pTAK_left_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
-Python Score = 8
-Java Score = 37
-Number of Files = 62
-File: /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 420, in command_line_converter
- doc3 = convert2to3(doc2, [namespace] if namespace else [], args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 83, in convert2to3
- return sbol_utilities.sbol3_sbol2_conversion.convert2to3(sbol2_doc, namespaces)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 821, in convert2to3
- converter = SBOL2To3ConversionVisitor(doc2, namespaces)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 436, in __init__
- self._convert(doc2)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 441, in _convert
- self.visit_document(doc2)
- ~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 609, in visit_document
- self.visit_component_definition(obj)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 583, in visit_component_definition
- f, locations = self.visit_sequence_annotation(sa2)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 783, in visit_sequence_annotation
- raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
-NotImplementedError: Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://sbols.org/v2#displayId, BBa_C0051_annotation
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://sbols.org/v2#displayId, Reporter_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#displayId, BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/partseq_156, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_C0051
- http://www.async.ece.utah.edu/Repressor1/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/partseq_156, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_156
- http://www.async.ece.utah.edu/pTAKRightCasette, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://www.w3.org/ns/prov#wasDerivedFrom, urn:0a9f5ec9-e70e-4ed1-93b1-50d4b8b1a36c
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/seq/partseq_185
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:b6aaf954-c531-4788-9dd9-7280a2c5e5cd
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pTAKRightCasette, http://purl.org/dc/terms/title, pTAK Right Casette
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:73812e7c-1423-4599-814a-f95d66dbe560
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://sbols.org/v2#displayId, _0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator
- http://www.async.ece.utah.edu/BBa_C0051, http://purl.org/dc/terms/title, cI lam
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#displayId, rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/BBa_C0051, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#displayId, Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/ns/prov#wasDerivedFrom, urn:8ea910ca-5b5e-4d3e-a752-f9afa578a48c
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/rbsB, http://www.w3.org/ns/prov#wasDerivedFrom, urn:afb8189e-cb6e-499f-9f12-7113d3767d1a
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://sbols.org/v2#displayId, RBS_cons_BBa_C0051
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Reporter
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#elements, caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacaca
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter, http://sbols.org/v2#displayId, Reporter
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://sbols.org/v2#displayId, BBa_R0010_annotation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000141
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/BBa_C0051
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#displayId, partseq_185
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:684c85a5-7603-4f3e-9cf2-102af55dc66a
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_E0040
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d0ca1539-371f-48b5-8e26-d27fa1693e5b
- http://www.async.ece.utah.edu/pTAKRightCasette, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d2627b90-1b94-432a-aa40-27631bd0a02a
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://sbols.org/v2#displayId, Reporter_cons_Terminator
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Reporter/rbsB
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/description, promoter (lacI regulated)
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/partseq_156, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_156
- http://www.async.ece.utah.edu/BBa_E0040, http://www.w3.org/ns/prov#wasDerivedFrom, urn:0fb4a103-86c4-4d90-8e73-d35ca45b4cf7
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://sbols.org/v2#displayId, Repressor1_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#displayId, RBS
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000139
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/ns/prov#wasDerivedFrom, urn:2601affa-e0fd-4362-a23e-e772675a6d19
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://sbols.org/v2#elements, atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051, http://sbols.org/v2#displayId, BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#displayId, BBa_E0040
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/title, GFP
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#displayId, Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#displayId, RBS_annotation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:806ac4b0-ab0f-4ab4-aa33-9edc8a427c2f
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#displayId, Terminator
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#displayId, pTAKRightCasette
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#displayId, BBa_E0040_annotation
- http://www.async.ece.utah.edu/partseq_156, http://sbols.org/v2#displayId, partseq_156
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1
- http://www.async.ece.utah.edu/BBa_E0040, http://purl.org/dc/terms/description, green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP (SwissProt: P42212
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Terminator
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#displayId, rbsB
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_R0010
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/rbsB_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/BBa_R0010
- http://www.async.ece.utah.edu/Reporter, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation
- http://www.async.ece.utah.edu/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/ns/prov#wasDerivedFrom, urn:c978bfae-0463-483e-8170-6a20e3968474
- http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#end, 200
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/Repressor1/RBS
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:d5318bf5-9526-4ed9-a7e7-2a58d7e428dd
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://sbols.org/v2#displayId, rbsB_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation
- http://www.async.ece.utah.edu/partseq_156, http://sbols.org/v2#elements, atgagcacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcgctgcaaacgacgaaaactacgctttagtagcttaataa
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/BBa_C0051
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Terminator, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/Repressor1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#object, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter
- http://www.async.ece.utah.edu/Reporter/rbsB, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/rbsB
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://sbols.org/v2#displayId, Terminator_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#displayId, BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation, http://sbols.org/v2#component, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation
- http://www.async.ece.utah.edu/BBa_R0010, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://sbols.org/v2#subject, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#definition, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceConstraint
- http://www.async.ece.utah.edu/BBa_C0051, http://www.w3.org/ns/prov#wasDerivedFrom, http://partsregistry.org/part/BBa_C0051
- http://www.async.ece.utah.edu/RBS, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/Reporter/BBa_E0040, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Reporter/BBa_E0040
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010, http://sbols.org/v2#displayId, BBa_R0010
- http://www.async.ece.utah.edu/Repressor1/RBS, http://sbols.org/v2#access, http://sbols.org/v2#public
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:579d86e8-e769-4195-bc11-5f2c1f52f8fa
- http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_annotation/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/BBa_R0010, http://purl.org/dc/terms/title, LacI
- http://www.async.ece.utah.edu/partseq_185, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/Reporter/rbsB, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/BBa_C0051, http://purl.org/dc/terms/description, cI repressor from E. coli phage lambda (+LVA)
- http://www.async.ece.utah.edu/RBS, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/RBS
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000987
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#GenericLocation
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation, http://sbols.org/v2#location, http://www.async.ece.utah.edu/Repressor1/BBa_C0051_annotation/genericLocation
- http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051, http://sbols.org/v2#object, http://www.async.ece.utah.edu/Repressor1/BBa_C0051
- http://www.async.ece.utah.edu/BBa_E0040, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/Terminator, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter, http://sbols.org/v2#restriction, http://sbols.org/v2#precedes
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/BBa_C0051, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/partseq_156
- http://www.async.ece.utah.edu/Reporter/rbsB_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:8b82f7d0-48f0-4162-8f15-56d25bea5879
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/Repressor1/BBa_C0051
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_annotation
- http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_annotation, http://www.w3.org/ns/prov#wasDerivedFrom, urn:61856bd6-408c-4621-9a5e-89889378654e
- http://www.async.ece.utah.edu/Repressor1/BBa_C0051, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Component
- http://www.async.ece.utah.edu/Reporter, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pTAKRightCasette, http://sbols.org/v2#sequenceConstraint, http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter
- http://www.async.ece.utah.edu/Repressor1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/Repressor1/RBS_annotation
- http://www.async.ece.utah.edu/Repressor1/RBS_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pTAKRightCasette/Terminator_annotation/genericLocation
- http://www.async.ece.utah.edu/Reporter/BBa_E0040_annotation/genericLocation, http://sbols.org/v2#displayId, genericLocation
- http://www.async.ece.utah.edu/partseq_156, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/partseq_185, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/partseq_185
- http://www.async.ece.utah.edu/rbsB, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:00 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:01 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Exception in thread "main" org.sbolstandard.core3.util.SBOLGraphException: Could not validate the SBOL document:
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:750, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/partseq_156,
- Value: [http://www.async.ece.utah.edu/Repressor1/BBa_C0051/genericLocation],
- Property: components[1].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/BBa_C0051,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, 200], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010/range],
- Property: components[6].constraints[0].subject[http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010_cons_Repressor1,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pTAKRightCasette/Reporter/genericLocation],
- Property: components[6].constraints[2].subject[http://www.async.ece.utah.edu/pTAKRightCasette/Reporter].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pTAKRightCasette/Reporter_cons_Terminator,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Repressor1/RBS/genericLocation],
- Property: components[1].constraints[0].subject[http://www.async.ece.utah.edu/Repressor1/RBS].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Repressor1/RBS_cons_BBa_C0051,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1/genericLocation],
- Property: components[6].constraints[1].subject[http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/pTAKRightCasette/Repressor1_cons_Reporter,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-11402 - The value of the end property of a Range MUST be greater than zero and less than or equal to the length of the elements value of theSequence referred to by its hasSequence property.,
- Value: 200,
- Property: components[6].subComponents[3].locations[0].end,
- Entity URI: http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
-
-sbol3-11706 - If the restriction property of a Constraint is drawn from Table 10 and if the Feature objects referred to by the subject and object properties both have hasLocation properties with Location objects whose hasSequence property refers to the same Sequence, then the positions of the referred Location objects MUST comply with the relation specified in Table 10.
- ADDITIONAL INFORMATION = Restriction:http://sbols.org/v3#precedes, Calculated Subject Location: [1, -1], Calculated Object Location:[1, -1],
- Value: [http://www.async.ece.utah.edu/Reporter/rbsB/genericLocation],
- Property: components[4].constraints[0].subject[http://www.async.ece.utah.edu/Reporter/rbsB].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/rbsB_cons_BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.Constraint
-
-sbol3-10807 - If a SubComponent object has at least one hasLocation and zero sourceLocation properties, and the Component linked by its instanceOf has precisely one hasSequence property whose Sequence has a value for its elements property, then the sum of the lengths of the Location objects referred to by the hasLocation properties MUST equal the length of the elements value of the Sequence. ADDITIONAL INFORMATION: Sequence length:720, Calculated location length:0, Sequence: http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c,
- Value: [http://www.async.ece.utah.edu/Reporter/BBa_E0040/genericLocation],
- Property: components[4].subComponents[1].hasLocation,
- Entity URI: http://www.async.ece.utah.edu/Reporter/BBa_E0040,
- Entity Type: class org.sbolstandard.core3.entity.SubComponent
-
-sbol3-11401 - The value of the start property of a Range MUST be greater than zero and less than or equal to the length of the elements value of the Sequence referred to by its hasSequence property.,
- Value: 1,
- Property: components[6].subComponents[3].locations[0].start,
- Entity URI: http://www.async.ece.utah.edu/pTAKRightCasette/BBa_R0010/range,
- Entity Type: class org.sbolstandard.core3.entity.Range
- at org.sbolstandard.core3.validation.SBOLValidator.isValid(SBOLValidator.java:110)
- at org.sbolstandard.core3.io.SBOLIO.assertValid(SBOLIO.java:42)
- at org.sbolstandard.core3.io.SBOLIO.read(SBOLIO.java:149)
- at org.sbolstandard.converter.App.main(App.java:304)
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Namespace {http://sbols.org/genBankConversion#} not found in partial_pTAK_right_cassette.xml
-Namespace {http://www.ncbi.nlm.nih.gov/genbank#} not found in partial_pTAK_right_cassette.xml
-ComponentDefinition http://www.async.ece.utah.edu/RBS not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_C0051 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Terminator not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_E0040 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Repressor1 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Reporter not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/BBa_R0010 not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/pTAKRightCasette not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/rbsB not found in java32.xml
-ComponentDefinition http://www.async.ece.utah.edu/Exported_File not found in partial_pTAK_right_cassette.xml
-Sequence http://www.async.ece.utah.edu/partseq_156 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/_0a9f5ec9_e70e_4ed1_93b1_50d4b8b1a36c not found in java32.xml
-Sequence http://www.async.ece.utah.edu/partseq_185 not found in java32.xml
-Sequence http://www.async.ece.utah.edu/Exported_File_seq not found in partial_pTAK_right_cassette.xml
-Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
-Python Score = 8
-Java Score = 37
-Number of Files = 63
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH37326.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH37326.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation4/range
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation6
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://sbols.org/v2#start, 2483
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://sbols.org/v2#end, 2843
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://sbols.org/v2#end, 1724
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://sbols.org/v2#end, 92
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH37326_seq
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/genBankConversion#note, bla gene promoter
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://sbols.org/v2#start, 1913
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation3/range
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation2/range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation13
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation7/range
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation9/range
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation0/range
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://purl.org/dc/terms/title, 30791fwd
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/v2#displayId, annotation12
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation3/range
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/genBankConversion#label, pUC rev
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/genBankConversion#label, pUC_seq F
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://purl.org/dc/terms/title, pUC_seq F
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH37326_seq, http://sbols.org/v2#elements, TTTGGTCTCAAATGGCTACTCAACGAAGGGCAAACCCTAGCTCTCTCCATCTAATTACTGTATTCTCTCTGCTCGTCGCTGTCGTCTCAGGTTGAGACCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGAGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCC
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://sbols.org/v2#end, 1936
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/genBankConversion#label, AGGT 4bp overhang
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation9/range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/v2#displayId, annotation13
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://sbols.org/v2#start, 12
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://purl.org/dc/terms/title, 30791rev
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation11
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation1/range
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation9
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://sbols.org/v2#end, 92
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation7/range
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation8/range
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/v2#displayId, annotation10
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://sbols.org/v2#end, 2497
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://sbols.org/v2#start, 2478
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://sbols.org/v2#end, 2848
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/v2#displayId, annotation8
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://sbols.org/v2#start, 2827
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://purl.org/dc/terms/title, P(LAC)
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation8/range
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation0
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation1
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation8
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#displayId, pICH37326
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation4/range
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation13/range
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/genBankConversion#gene, Sm/Sp
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation13/range
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/v2#displayId, annotation11
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation7
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/genBankConversion#SECDrawAs, Gene
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://sbols.org/v2#end, 2483
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/genBankConversion#label, pUC fwd
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/genBankConversion#label, P(BLA)
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/genBankConversion#label, 30791fwd
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation11/range
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/genBankConversion#label, kanseqr
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH37326, http://www.ncbi.nlm.nih.gov/genbank#date, 10-JUN-2008
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation6/range
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://sbols.org/v2#end, 635
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://sbols.org/v2#start, 714
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation3
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation2/range, http://sbols.org/v2#start, 89
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation10/range
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/genBankConversion#label, Sm/Sp
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://sbols.org/v2#start, 610
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://purl.org/dc/terms/title, Sm/Sp
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation12
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH37326
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation9/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation11
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation10/range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation9
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation1
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://sbols.org/v2#start, 679
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326_seq
- http://www.async.ece.utah.edu/pICH37326/annotation8/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation10
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation10
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation2/range
- http://www.async.ece.utah.edu/pICH37326, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://sbols.org/v2#start, 2843
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation3
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation12/range
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://sbols.org/v2#start, 105
- http://www.async.ece.utah.edu/pICH37326/annotation3/range, http://sbols.org/v2#end, 124
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://purl.org/dc/terms/title, AGGT 4bp overhang
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation5
- http://www.async.ece.utah.edu/pICH37326/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation1/range
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation5/range
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation13
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation2
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation11/range
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation7
- http://www.async.ece.utah.edu/pICH37326, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH37326/annotation10/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation4
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://purl.org/dc/terms/title, calreticulin apoplast targeting signal VSG
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH37326, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH37326/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/v2#displayId, annotation9
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation0
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://sbols.org/v2#end, 2926
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation12
- http://www.async.ece.utah.edu/pICH37326/annotation6/range, http://sbols.org/v2#end, 679
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/genBankConversion#label, 30791rev
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation2
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation8
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://sbols.org/genBankConversion#label, kanseqf
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326/annotation9, http://purl.org/dc/terms/title, kanseqf
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/genBankConversion#label, P(LAC)
- http://www.async.ece.utah.edu/pICH37326/annotation13/range, http://sbols.org/v2#start, 2907
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation5/range
- http://www.async.ece.utah.edu/pICH37326/annotation11, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://sbols.org/v2#end, 670
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://sbols.org/v2#start, 11
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://sbols.org/v2#end, 14
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation4
- http://www.async.ece.utah.edu/pICH37326/annotation3, http://purl.org/dc/terms/title, pUC fwd
- http://www.async.ece.utah.edu/pICH37326_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH37326/annotation10, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH37326/annotation12/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation12/range
- http://www.async.ece.utah.edu/pICH37326_seq, http://sbols.org/v2#displayId, pICH37326_seq
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation0/range
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://purl.org/dc/terms/title, P(BLA)
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37326_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://purl.org/dc/terms/title, pUC rev
- http://www.async.ece.utah.edu/pICH37326/annotation8, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37326/annotation5/range, http://sbols.org/v2#start, 651
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://purl.org/dc/terms/title, kanseqr
- http://www.async.ece.utah.edu/pICH37326/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37326/annotation6/range
- http://www.async.ece.utah.edu/pICH37326/annotation11/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37326/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH37326/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37326/annotation13, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37326, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37326/annotation6
- http://www.async.ece.utah.edu/pICH37326/annotation1, http://sbols.org/genBankConversion#label, calreticulin apoplast targeting signal VSG
- http://www.async.ece.utah.edu/pICH37326/annotation12, http://sbols.org/genBankConversion#note, lac promoter
- http://www.async.ece.utah.edu/pICH37326/annotation7, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH37326/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37326/annotation5
- http://www.async.ece.utah.edu/pICH37326/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH37326.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH37326.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:03 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:04 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH37326.xml
-Python Score = 8
-Java Score = 38
-Number of Files = 64
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH37431.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH37431.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation8
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation5/range
- http://www.async.ece.utah.edu/pICH37431, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://purl.org/dc/terms/title, kanseqf
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation7
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation5/range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation12
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation5
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://sbols.org/v2#end, 2480
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://sbols.org/v2#end, 14
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/genBankConversion#label, pUC_seq F
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/genBankConversion#label, RAmy3A SP (Oryza sativa)
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation1/range
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation4/range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation2
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation3/range
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation11
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/v2#displayId, annotation10
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/genBankConversion#label, pUC fwd
- http://www.async.ece.utah.edu/pICH37431_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://sbols.org/v2#start, 2904
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/genBankConversion#gene, Sm/Sp
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://purl.org/dc/terms/title, P(BLA)
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation2/range
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/v2#displayId, annotation13
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation4/range
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://sbols.org/v2#start, 11
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://sbols.org/v2#start, 2480
- http://www.async.ece.utah.edu/pICH37431, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://sbols.org/v2#start, 2824
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation13
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://sbols.org/v2#end, 89
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation6/range
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation1
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation4
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation12/range
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation13
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://purl.org/dc/terms/title, AGGT 4bp overhang
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation2
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://sbols.org/v2#end, 1721
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://sbols.org/v2#start, 676
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation10
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://purl.org/dc/terms/title, RAmy3A SP (Oryza sativa)
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation8/range
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation8/range
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/genBankConversion#label, 30791fwd
- http://www.async.ece.utah.edu/pICH37431_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431_seq
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation9
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation10/range
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://sbols.org/v2#end, 89
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/genBankConversion#label, AGGT 4bp overhang
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://sbols.org/v2#start, 102
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431, http://www.ncbi.nlm.nih.gov/genbank#date, 7-JUL-2008
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation4
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation9
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://sbols.org/v2#end, 667
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://purl.org/dc/terms/title, pUC rev
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://sbols.org/v2#end, 676
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://sbols.org/v2#start, 607
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://purl.org/dc/terms/title, P(LAC)
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/v2#displayId, annotation12
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation6
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation6/range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation12/range
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation11/range
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation2/range
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/v2#displayId, annotation8
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://purl.org/dc/terms/title, pUC_seq F
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/genBankConversion#label, Sm/Sp
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/genBankConversion#label, P(LAC)
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://sbols.org/v2#start, 648
- http://www.async.ece.utah.edu/pICH37431/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://sbols.org/v2#end, 2923
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation12
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://sbols.org/v2#start, 1910
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/genBankConversion#label, kanseqf
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation1
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation1/range
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation9/range
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation3/range
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation0
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://sbols.org/v2#start, 711
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://purl.org/dc/terms/title, pUC fwd
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/genBankConversion#label, 30791rev
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/genBankConversion#note, lac promoter
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://sbols.org/v2#end, 1933
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/genBankConversion#label, kanseqr
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation0/range
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation5
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation7/range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH37431/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://sbols.org/v2#start, 12
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/genBankConversion#label, P(BLA)
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation8/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation0/range
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/v2#displayId, annotation11
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation6
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://sbols.org/v2#end, 2494
- http://www.async.ece.utah.edu/pICH37431/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH37431_seq, http://sbols.org/v2#displayId, pICH37431_seq
- http://www.async.ece.utah.edu/pICH37431/annotation4, http://purl.org/dc/terms/title, 30791fwd
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation11/range
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH37431/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH37431
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation8
- http://www.async.ece.utah.edu/pICH37431/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/genBankConversion#note, bla gene promoter
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://purl.org/dc/terms/title, kanseqr
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation7/range
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation3
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation10
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH37431_seq
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://sbols.org/v2#end, 2840
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation3
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation9/range, http://sbols.org/v2#start, 2475
- http://www.async.ece.utah.edu/pICH37431/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation13/range
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://sbols.org/genBankConversion#SECDrawAs, Gene
- http://www.async.ece.utah.edu/pICH37431/annotation10, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH37431_seq, http://sbols.org/v2#elements, TTTGGTCTCAAATGGGGAAGCAAATGGCCGCCCTGTGTGGCTTTCTCCTCGTGGCGTTGCTCTGGCTCACGCCCGACGTCGCGTCAGGTTGAGACCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGAGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCC
- http://www.async.ece.utah.edu/pICH37431, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH37431/annotation4/range, http://sbols.org/v2#end, 632
- http://www.async.ece.utah.edu/pICH37431/annotation11/range, http://sbols.org/v2#end, 2845
- http://www.async.ece.utah.edu/pICH37431/annotation10/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation10/range
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation7, http://purl.org/dc/terms/title, Sm/Sp
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://sbols.org/v2#end, 121
- http://www.async.ece.utah.edu/pICH37431/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://sbols.org/genBankConversion#vntifkey, 27
- http://www.async.ece.utah.edu/pICH37431/annotation3, http://sbols.org/genBankConversion#featureType, Primer
- http://www.async.ece.utah.edu/pICH37431/annotation13, http://sbols.org/genBankConversion#label, pUC rev
- http://www.async.ece.utah.edu/pICH37431/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/v2#displayId, annotation9
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation7
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://sbols.org/v2#start, 2840
- http://www.async.ece.utah.edu/pICH37431/annotation12/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH37431/annotation6, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH37431/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH37431/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH37431/annotation13/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation13/range
- http://www.async.ece.utah.edu/pICH37431/annotation11, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH37431/annotation11
- http://www.async.ece.utah.edu/pICH37431/annotation2/range, http://sbols.org/v2#start, 86
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#displayId, pICH37431
- http://www.async.ece.utah.edu/pICH37431, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH37431/annotation0
- http://www.async.ece.utah.edu/pICH37431/annotation8, http://purl.org/dc/terms/title, 30791rev
- http://www.async.ece.utah.edu/pICH37431/annotation12, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH37431/annotation9, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH37431/annotation9/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH37431.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH37431.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:06 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:07 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH37431.xml
-Python Score = 8
-Java Score = 39
-Number of Files = 65
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41373.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41373.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://sbols.org/v2#start, 3583
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation4/range
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation2
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation5/range
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation5
- http://www.async.ece.utah.edu/pICH41373_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGAATTCCAATCCCACAAAAATCTGAGCTTAACAGCACAGTTGCTCCTCTCAGAGCAGAATCGGGTATTCAACACCCTCATATCAACTACTACGTTGTGTATAACGGTCCACATGCCGGTATATACGATGACTGGGGTTGTACAAAGGCGGCAACAAACGGCGTTCCCGGAGTTGCACACAAGAAATTTGCCACTATTACAGAGGCAAGAGCAGCAGCTGACGCGTACACAACAAGTCAGCAAACAGACAGGTTGAACTTCATCCCCAAAGGAGAAGCTCAACTCAAGCCCAAGAGCTTTGCTAAGGCCCTAACAAGCCCACCAAAGCAAAAAGCCCACTGGCTCACGCTAGGAACCAAAAGGCCCAGCAGTGATCCAGCCCCAAAAGAGATCTCCTTTGCCCCGGAGATTACAATGGACGATTTCCTCTATCTTTACGATCTAGGAAGGAAGTTCGAAGGTGAAGGTGACGACACTATGTTCACCACTGATAATGAGAAGGTTAGCCTCTTCAATTTCAGAAAGAATGCTGACCCACAGATGGTTAGAGAGGCCTACGCAGCAAGTCTCATCAAGACGATCTACCCGAGTAACAATCTCCAGGAGATCAAATACCTTCCCAAGAAGGTTAAAGATGCAGTCAAAAGATTCAGGACTAATTGCATCAAGAACACAGAGAAAGACATATTTCTCAAGATCAGAAGTACTATTCCAGTATGGACGATTCAAGGCTTGCTTCATAAACCAAGGCAAGTAATAGAGATTGGAGTCTCTAAAAAGGTAGTTCCTACTGAATCTAAGGCCATGCATGGAGTCTAAGATTCAAATCGAGGATCTAACAGAACTCGCCGTCAAGACTGGCGAACAGTTCATACAGAGTCTTTTACGACTCAATGACAAGAAGAAAATCTTCGTCAACATGGTGGAGCACGACACTCTGGTCTACTCCAAAAATGTCAAAGATACAGTCTCAGAAGATCAAAGGGCTATTGAGACTTTTCAACAAAGGATAATTTCGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAGTAGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCATTCAAGATCTCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGAGGTTCCAACCACGTCTACAAAGCAAGTGGATTGATGTGACATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACACGC
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation3/range
- http://www.async.ece.utah.edu/pICH41373, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://purl.org/dc/terms/title, 35S promoter (no BpiI and BsaI)
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH41373, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation0
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41373_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation4/range
- http://www.async.ece.utah.edu/pICH41373, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41373_seq
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation1/range
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation2
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation0/range
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation3
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41373_seq, http://sbols.org/v2#displayId, pICH41373_seq
- http://www.async.ece.utah.edu/pICH41373, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation0
- http://www.async.ece.utah.edu/pICH41373/annotation0/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#displayId, pICH41373
- http://www.async.ece.utah.edu/pICH41373, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41373
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/genBankConversion#label, 35S promoter (no BpiI and BsaI)
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation0/range
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation4
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/genBankConversion#label, CaMV 35s 5'UT
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41373_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373_seq
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation1
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://sbols.org/v2#end, 3589
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41373/annotation1/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation3
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation1/range
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation5
- http://www.async.ece.utah.edu/pICH41373/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41373/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation4
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation3/range
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://purl.org/dc/terms/title, CaMV 35s 5'UT
- http://www.async.ece.utah.edu/pICH41373/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41373/annotation1, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41373/annotation1
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation2/range
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41373/annotation2/range
- http://www.async.ece.utah.edu/pICH41373/annotation5, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41373/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373, http://www.ncbi.nlm.nih.gov/genbank#date, 17-MAR-2009
- http://www.async.ece.utah.edu/pICH41373, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41373/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41373/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41373/annotation5/range
- http://www.async.ece.utah.edu/pICH41373/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41373/annotation5/range, http://sbols.org/v2#end, 3589
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41373.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41373.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:09 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:10 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41373.xml
-Python Score = 8
-Java Score = 40
-Number of Files = 66
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41388.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41388.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/genBankConversion#featureType, Source
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation5
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation4/range
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://sbols.org/v2#end, 2677
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41388, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41388
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation3/range
- http://www.async.ece.utah.edu/pICH41388_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388_seq
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://purl.org/dc/terms/title, Source
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation6/range
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation6
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation4/range
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation0
- http://www.async.ece.utah.edu/pICH41388, http://www.ncbi.nlm.nih.gov/genbank#date, 30-NOV-2009
- http://www.async.ece.utah.edu/pICH41388_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41388_seq
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation0/range
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/genBankConversion#dnas_title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/genBankConversion#dnas_title, pICH41388
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation5
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation3
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation2
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://sbols.org/v2#end, 2677
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation1
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#displayId, pICH41388
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation5/range
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/genBankConversion#dnas_title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41388, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation2
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation1/range
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation3
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/genBankConversion#label, 35S pro short (no BpiI and BsaI)
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation1/range
- http://www.async.ece.utah.edu/pICH41388, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation4
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388_seq, http://sbols.org/v2#displayId, pICH41388_seq
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/genBankConversion#dnas_title, G to A
- http://www.async.ece.utah.edu/pICH41388/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation2/range
- http://www.async.ece.utah.edu/pICH41388/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation0
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://purl.org/dc/terms/title, CaMV 35s 5'UT
- http://www.async.ece.utah.edu/pICH41388/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation2/range
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/genBankConversion#dnas_title, ORI
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation3/range
- http://www.async.ece.utah.edu/pICH41388/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://purl.org/dc/terms/title, 35S pro short (no BpiI and BsaI)
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation4
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41388/annotation1
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41388/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://sbols.org/v2#start, 2671
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation6
- http://www.async.ece.utah.edu/pICH41388/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41388_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGTCAACATGGTGGAGCACGACACTCTGGTCTACTCCAAAAATGTCAAAGATACAGTCTCAGAAGATCAAAGGGCTATTGAGACTTTTCAACAAAGGATAATTTCGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAGTAGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCATTCAAGATCTCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGAGGTTCCAACCACGTCTACAAAGCAAGTGGATTGATGTGACATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACACGC
- http://www.async.ece.utah.edu/pICH41388/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41388, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/genBankConversion#dnas_title, 35S pro short (no BpiI and BsaI)
- http://www.async.ece.utah.edu/pICH41388/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH41388/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation0/range
- http://www.async.ece.utah.edu/pICH41388/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41388/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://sbols.org/v2#end, 2677
- http://www.async.ece.utah.edu/pICH41388/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41388/annotation6/range
- http://www.async.ece.utah.edu/pICH41388/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41388/annotation5/range
- http://www.async.ece.utah.edu/pICH41388/annotation6, http://sbols.org/genBankConversion#label, CaMV 35s 5'UT
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41388.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41388.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:12 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:12 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41388.xml
-Python Score = 8
-Java Score = 41
-Number of Files = 67
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41402.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41402.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation0
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/genBankConversion#label, omega (TMV)
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation1/range
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation3/range
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation0
- http://www.async.ece.utah.edu/pICH41402_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41402, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation2
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation1
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation5/range
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation6
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41402_seq
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#displayId, pICH41402
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation1/range
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://purl.org/dc/terms/title, omega (TMV)
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41402, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation1
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation0/range
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation0/range
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation4/range
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation3
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation4/range
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation5
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41402/annotation4
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH41402, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41402, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41402/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation6
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41402_seq, http://sbols.org/v2#displayId, pICH41402_seq
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41402/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH41402, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41402
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41402_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402_seq
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation5/range
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation3/range
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation3
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation2/range
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41402/annotation6/range
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH41402_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTACTATTTACAATTAC
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH41402/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation2/range
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://sbols.org/v2#end, 2318
- http://www.async.ece.utah.edu/pICH41402/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41402/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation6/range
- http://www.async.ece.utah.edu/pICH41402_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41402/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation4
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation5
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41402/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41402/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41402/annotation2
- http://www.async.ece.utah.edu/pICH41402/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41402/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41402/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41402, http://www.ncbi.nlm.nih.gov/genbank#date, 27-MAY-2009
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41402.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41402.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:15 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:15 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41402.xml
-Python Score = 8
-Java Score = 42
-Number of Files = 68
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41414.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41414.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41414, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41414
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/genBankConversion#label, 35S ter
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation5
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/genBankConversion#dnas_title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41414_seq, http://sbols.org/v2#elements, CGCTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGCTTCTCTAGCTAGAGTCGATCGACAAGCTCGAGTTTCTCCATAATAATGTGTGAGTAGTTCCCAGATAAGGGAATTAGGGTTCCTATAGGGTTTCGCTCATGTGTTGAGCATATAAGAAACCCTTAGTATGTATTTGTATTTGTAAAATACTTCTATCAATAAAATTTCTAATTCCTAAAACCAAAATCCAGTACTAAAATCCAGAT
- http://www.async.ece.utah.edu/pICH41414_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/genBankConversion#dnas_title, 35S ter
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation1
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/genBankConversion#label, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH41414, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation6
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation4/range
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation5
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation0
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation3
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation2
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/genBankConversion#featureType, MIsc._Feature
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation1
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation3
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414_seq
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation4
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation3/range
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation2/range
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation0/range
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation6/range
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation1/range
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/genBankConversion#dnas_title, ORI
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#displayId, pICH41414
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation5/range
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41414/annotation6
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation3/range
- http://www.async.ece.utah.edu/pICH41414/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://purl.org/dc/terms/title, CGCT 4bp overhang
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation5/range
- http://www.async.ece.utah.edu/pICH41414, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation6/range
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/genBankConversion#vntifkey, 43
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/genBankConversion#dnas_title, G to A
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation1/range
- http://www.async.ece.utah.edu/pICH41414, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://sbols.org/v2#end, 2455
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation2/range
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41414, http://www.ncbi.nlm.nih.gov/genbank#date, 18-JUN-2009
- http://www.async.ece.utah.edu/pICH41414, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41414, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41414_seq
- http://www.async.ece.utah.edu/pICH41414_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://purl.org/dc/terms/title, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation4
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/genBankConversion#featureType, Terminator
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation2
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/genBankConversion#featureType, MIsc._Feature
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation0
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41414/annotation0/range
- http://www.async.ece.utah.edu/pICH41414_seq, http://sbols.org/v2#displayId, pICH41414_seq
- http://www.async.ece.utah.edu/pICH41414/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://purl.org/dc/terms/title, 35S ter
- http://www.async.ece.utah.edu/pICH41414/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41414/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41414/annotation4/range
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41414/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41414/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41414/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41414/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/genBankConversion#label, CGCT 4bp overhang
- http://www.async.ece.utah.edu/pICH41414/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41414/annotation3, http://sbols.org/genBankConversion#dnas_title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41414/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH41414/annotation1/range, http://sbols.org/v2#start, 231
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41414.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41414.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:18 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:18 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41414.xml
-Python Score = 8
-Java Score = 43
-Number of Files = 69
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41421.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41421.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://sbols.org/v2#start, 1192
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation0
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation6/range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#displayId, pICH41421
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation4
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41421, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://sbols.org/v2#start, 2232
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation0/range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://purl.org/dc/terms/title, nost
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation5
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation0
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/genBankConversion#featureType, Terminator
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://purl.org/dc/terms/title, CGCT
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://sbols.org/v2#end, 2498
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation3
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41421_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation4/range
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation1
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://purl.org/dc/terms/title, GCTT
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation5
- http://www.async.ece.utah.edu/pICH41421, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://sbols.org/v2#start, 1984
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41421, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41421
- http://www.async.ece.utah.edu/pICH41421_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation5/range
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://sbols.org/v2#end, 2502
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation2/range
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation6/range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation1
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://sbols.org/v2#start, 1385
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation3/range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation4
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://sbols.org/v2#start, 215
- http://www.async.ece.utah.edu/pICH41421, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation1/range
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/genBankConversion#label, CGCT
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41421/annotation4, http://sbols.org/genBankConversion#label, GCTT
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation1/range
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation4/range
- http://www.async.ece.utah.edu/pICH41421, http://www.ncbi.nlm.nih.gov/genbank#date, 7-APR-2009
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://sbols.org/v2#end, 2235
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation2
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation5/range
- http://www.async.ece.utah.edu/pICH41421_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421_seq
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://sbols.org/v2#end, 1999
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://sbols.org/v2#start, 2236
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41421/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation2/range
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41421_seq
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://sbols.org/v2#end, 1225
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation3
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41421/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41421/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation6
- http://www.async.ece.utah.edu/pICH41421/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41421/annotation0/range
- http://www.async.ece.utah.edu/pICH41421/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation6
- http://www.async.ece.utah.edu/pICH41421/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://sbols.org/v2#end, 1984
- http://www.async.ece.utah.edu/pICH41421_seq, http://sbols.org/v2#displayId, pICH41421_seq
- http://www.async.ece.utah.edu/pICH41421_seq, http://sbols.org/v2#elements, GTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGCTTGTCAAGCAGATCGTTCAAACATTTGGCAATAAAGTTTCTTAAGATTGAATCCTGTTGCCGGTCTTGCGATGATTATCATATAATTTCTGTTGAATTACGTTAAGCATGTAATAATTAACATGTAATGCATGACGTTATTTATGAGATGGGTTTTTATGATTAGAGTCCCGCAATTATACATTTAATACGCGATAGAAAACAAAATATAGCGCGCAAACTAGGATAAATTATCGCGCGCGGTGTCATCTATGTTACTAGATCGACGCTTGAGACCACGAA
- http://www.async.ece.utah.edu/pICH41421/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41421/annotation3/range
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://sbols.org/v2#start, 2499
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/genBankConversion#vntifkey, 43
- http://www.async.ece.utah.edu/pICH41421, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41421/annotation3, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41421/annotation1, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41421/annotation0, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41421/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41421, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41421/annotation2
- http://www.async.ece.utah.edu/pICH41421/annotation5, http://sbols.org/genBankConversion#label, nost
- http://www.async.ece.utah.edu/pICH41421/annotation1/range, http://sbols.org/v2#end, 1192
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41421.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41421.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:21 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:21 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41421.xml
-Python Score = 8
-Java Score = 44
-Number of Files = 70
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41432.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41432.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://sbols.org/v2#start, 1192
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#displayId, pICH41432
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://sbols.org/v2#end, 1999
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation1/range
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://sbols.org/v2#start, 2950
- http://www.async.ece.utah.edu/pICH41432_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://sbols.org/v2#end, 2949
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://sbols.org/v2#start, 2236
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation3
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://sbols.org/v2#start, 2232
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation0
- http://www.async.ece.utah.edu/pICH41432, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation3/range
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/genBankConversion#vntifkey, 43
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation5/range
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41432, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41432
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41432_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432_seq
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://purl.org/dc/terms/title, ocst
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/genBankConversion#featureType, Terminator
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation4
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation5/range
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation1/range
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation1
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://sbols.org/v2#end, 1192
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation6/range
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation0
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation4
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation0/range
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation2/range
- http://www.async.ece.utah.edu/pICH41432, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation6
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation3/range
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://sbols.org/v2#end, 1225
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation5
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://sbols.org/v2#end, 2235
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41432_seq, http://sbols.org/v2#displayId, pICH41432_seq
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation1
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://sbols.org/v2#end, 1984
- http://www.async.ece.utah.edu/pICH41432_seq, http://sbols.org/v2#elements, GTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGCTTGTCCTGCTTTAATGAGATATGCGAGAAGCCTATGATCGCATGATATTTGCTTTCAATTCTGTTGTGCACGTTGTAAAAAACCTGAGCATGTGTAGCTCAGATCCTTACCGCCGGTTTCGGTTCATTCTAATGAATATATCACCCGTTACTATCGTATTTTTATGAATAATATTCTCCGTTCAATTTACTGATTGTACCCTACTACTTATATGTACAATATTAAAATGAAAACAATATATTGTGCTGAATAGGTTTATAGCGACATCTATGATAGAGCGCCACAATAACAAACAATTGCGTTTTATTATTACAAATCCAATTTTAAAAAAAGCGGCAGAACCGGTCAAACCTAAAAGACTGATTACATAAATCTTATTCAAATTTCAAAAGTGCCCCAGGGGCTAGTATCTACGACACACCGAGCGGCGAACTAATAACGCTCACTGAAGGGAACTCCGGTTCCCCGCCGGCGCGCATGGGTGAGATTCCTTGAAGTTGAGTATTGGCCGTCCGCTCTACCGAAAGTTACGGGCACCATTCAACCCGGTCCAGCACGGCGGCCGGGTAACCGACTTGCTGCCCCGAGAATTATGCAGCATTTTTTTGGTGTATGTGGGCCCCAAATGAAGTGCAGGTCAAACCTTGACAGTGACGACAAATCGTTGGGCGGGTCCAGGGCGAATTTTGCGACAACATGTCGAGGCTCAGCAGGACCGCTTGAGACCACGAA
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://purl.org/dc/terms/title, CGCT
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/genBankConversion#label, GCTT
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://sbols.org/v2#start, 1385
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation4/range
- http://www.async.ece.utah.edu/pICH41432/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://sbols.org/v2#start, 1984
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41432_seq
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation0/range
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation6
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation3
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/genBankConversion#label, CGCT
- http://www.async.ece.utah.edu/pICH41432, http://www.ncbi.nlm.nih.gov/genbank#date, 15-MAY-2009
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432/annotation6/range, http://sbols.org/v2#end, 2953
- http://www.async.ece.utah.edu/pICH41432, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation5
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41432/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41432/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41432/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41432/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation4/range
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41432/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation2/range
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41432/annotation0/range, http://sbols.org/v2#start, 215
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41432/annotation6/range
- http://www.async.ece.utah.edu/pICH41432, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41432/annotation2
- http://www.async.ece.utah.edu/pICH41432/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41432/annotation2
- http://www.async.ece.utah.edu/pICH41432/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://purl.org/dc/terms/title, GCTT
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41432/annotation6, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41432/annotation5, http://sbols.org/genBankConversion#label, ocst
- http://www.async.ece.utah.edu/pICH41432/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41432.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41432.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:24 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:25 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41432.xml
-Python Score = 8
-Java Score = 45
-Number of Files = 71
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41531.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41531.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation0
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation0/range
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation3
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41531_seq
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://sbols.org/v2#end, 2235
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation6/range
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation3/range
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://sbols.org/v2#end, 1984
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41531, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41531
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://sbols.org/v2#start, 1192
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41531_seq, http://sbols.org/v2#displayId, pICH41531_seq
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation4/range
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation2/range
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation2
- http://www.async.ece.utah.edu/pICH41531_seq, http://sbols.org/v2#elements, GTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAAATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCAGCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCACGGCATGGACGAGCTGTACAAGTAAGCTTTGAGACCACGAA
- http://www.async.ece.utah.edu/pICH41531_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://sbols.org/v2#end, 1999
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation5
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://sbols.org/v2#start, 2953
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation5/range
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41531_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531_seq
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation1/range
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation6/range
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation2/range
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation5/range
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://sbols.org/v2#start, 215
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation1
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation3/range
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://sbols.org/v2#start, 2232
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41531, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation1/range
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation4/range
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation1
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/genBankConversion#label, GCTT
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation6
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/genBankConversion#label, AATG
- http://www.async.ece.utah.edu/pICH41531/annotation1/range, http://sbols.org/v2#end, 1192
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation3
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation0
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation4
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://purl.org/dc/terms/title, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH41531/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation4
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41531/annotation0/range
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41531/annotation6
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41531/annotation2/range, http://sbols.org/v2#start, 1385
- http://www.async.ece.utah.edu/pICH41531, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41531, http://www.ncbi.nlm.nih.gov/genbank#date, 7-APR-2009
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41531/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation5
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://sbols.org/v2#end, 2952
- http://www.async.ece.utah.edu/pICH41531/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41531, http://sbols.org/v2#displayId, pICH41531
- http://www.async.ece.utah.edu/pICH41531/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://sbols.org/genBankConversion#label, GFP
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://sbols.org/v2#end, 2956
- http://www.async.ece.utah.edu/pICH41531, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41531/annotation4, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH41531/annotation5, http://purl.org/dc/terms/title, GFP
- http://www.async.ece.utah.edu/pICH41531/annotation5/range, http://sbols.org/v2#start, 2233
- http://www.async.ece.utah.edu/pICH41531/annotation6, http://sbols.org/genBankConversion#label, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41531/annotation0/range, http://sbols.org/v2#end, 1225
- http://www.async.ece.utah.edu/pICH41531/annotation3/range, http://sbols.org/v2#start, 1984
- http://www.async.ece.utah.edu/pICH41531/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41531/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41531/annotation2
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41531.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41531.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:28 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:29 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41531.xml
-Python Score = 8
-Java Score = 46
-Number of Files = 72
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH41551.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41551.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation1/range
- http://www.async.ece.utah.edu/pICH41551_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551_seq
- http://www.async.ece.utah.edu/pICH41551, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation2
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH41551, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH41551
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/genBankConversion#label, pSTLS
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation4/range
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://sbols.org/v2#end, 2235
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://sbols.org/v2#end, 1984
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation2
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://sbols.org/v2#start, 1192
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation3
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation5
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://sbols.org/v2#start, 1385
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation0/range
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation5/range
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation2/range
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation3/range
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://sbols.org/v2#end, 1225
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://sbols.org/v2#end, 1192
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://sbols.org/v2#end, 3736
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation6
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://sbols.org/v2#start, 3733
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation6/range
- http://www.async.ece.utah.edu/pICH41551_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation3
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH41551, http://www.ncbi.nlm.nih.gov/genbank#date, 25-MAR-2009
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation0/range
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#displayId, pICH41551
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation5/range
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation1
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://sbols.org/v2#start, 215
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation4
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation2/range
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://purl.org/dc/terms/title, pSTLS
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://sbols.org/v2#end, 1999
- http://www.async.ece.utah.edu/pICH41551/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/genBankConversion#vntifkey, promoter
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation0
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41551/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH41551_seq
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH41551_seq, http://sbols.org/v2#displayId, pICH41551_seq
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation4/range
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH41551, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation4
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation0
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation1/range
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation5
- http://www.async.ece.utah.edu/pICH41551_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH41551_seq, http://sbols.org/v2#elements, GTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGTGTTCATCTGTTGGACAAGCTAATAATATCTATTTGTTGTCTGAATCACAATTTTCCCATGATAAATTAAAGCCAAAATTCGGCTTCTCACAACCTGATAGAATCTAATTTTATGACTTTTATCAAAAAAAAGAAGAAGATAGAATCTAATTTTATGACATTTAATGGTAGCCATTCCTTAAAAATTCCCGATTCAACTAATCCTTGGAGTTCATTTTCTCATAGGTGGATTTCATGCTGGAGTTACTGTAAATAGGGTTGGATTTCTACATTCTTGCGAGAGTGATCTGCATTCCAGCCCCCTCTGAAGCACAGGAGTCAGCTGCATTTCAAATGATTACCCAATTACAGACTATGGCAGACCGCACCCATTAGATTTAATGTGGCAAAGAAACATCAACTCCAATATTTTTGAATCCTATTAATGGCTATCATACCATAGTACTGTATTAGTACTGTCCAGAAGCAAAAATTGTTGTTTTAGAATATTACTTGGTTGCAACCGTATCAGTGCTTTGAACATTTATCAAGGCCAAATACATAATGGTGCCTTGAAATCAACTCTAGTTTATTGAAATGATGTCTATTGAGCACCTATATGTGTTGCCAGTATTGCCCATGCTTAACTTAGCATTCTGTTAACAAGTGTTATGCTGGATGTTCGAATCGAACATGGAGTTTTCATGTTGCTTAGAACTATATGCTTTCAGTGTTAGCAGTATCGGAAGGTAAATACAGTTTAAACACCAAAAGTAGAGAGAAATAAGGAGGAATTTAATCTTTGGATTTGATTCGTCTTTCTTGTGGGAATGGTGAACTCGTTAACCAGCTAGGTGAAATGAACTCAATACTTAGTTCAAAATTGTTTAAGTTCCATTTTTGGTTAAGAGAATTGAGTTGTGCTCTCTAGCTTTTGAAGATGATTTAGGTTCAAGGACTATAATTTTACACGATATTAGAGCTAGATCCATTGATAGGCCGCGTTTCTTAATGTTTTTGGCCTTGTAATTCTGTTTTCACATTGATTGACTGAATGAGTTGTGCTCTTTCTATATGATCTCGGATAATTCTTTTTCTCATGAGCTAACTTAAGTTAGGATATGAGCTAACTGCTCTCCAACAGGCAACAACCCATAGAGGAACCAATCAGTTTTTTCTTTTTGTCCTCCTCTTCCTTGCACGAGTGGACTTAGTAAATAGAAAGGAAAATAACAAAAATGTATAAGAAACAAGTCAATCTCTTGGGTCCCTTAATAATCAAAGAAAACCAATGAATGAACTCCAAGTGCACAAAACTAAGATAAGGCAAAGGAAAATAATTTGTAGTAAGAATGCTATATATTGATAATGTTGGTAATAATATTATCTAGAAGCAATCCACAGAAGGGGTGCCACGTGTCAACTTGTAAATCACAAATTGCAAGTCATCACTAATATTATTATCAAGGGACCATGCAAAGTGAAAATAAATAATTCATACTAAGTAGTGAGAGCAATACTTGAGACCACGAA
- http://www.async.ece.utah.edu/pICH41551/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation1
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation4, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://sbols.org/v2#end, 3732
- http://www.async.ece.utah.edu/pICH41551/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH41551/annotation6/range
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH41551/annotation3/range
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH41551/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH41551/annotation5, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH41551/annotation4/range, http://sbols.org/v2#start, 2232
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://sbols.org/v2#start, 2236
- http://www.async.ece.utah.edu/pICH41551/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH41551/annotation6, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH41551/annotation3, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://sbols.org/v2#start, 1984
- http://www.async.ece.utah.edu/pICH41551/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH41551/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH41551/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH41551, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH41551/annotation6
- http://www.async.ece.utah.edu/pICH41551, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH41551.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41551.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:31 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH41551.xml
-Python Score = 8
-Java Score = 47
-Number of Files = 73
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH42211.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42211.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://sbols.org/v2#end, 2511
- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#source,
- http://www.async.ece.utah.edu/pICH42211_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211_seq
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42211_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42211/annotation0/range
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#date, 24-APR-2009
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42211/annotation2/range
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42211/annotation4
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation3/range
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://sbols.org/v2#end, 1225
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation3
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/genBankConversion#label, rep\(pMB1)
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation0
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/genBankConversion#label, Sm/Sp\no\DraIII
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://sbols.org/v2#start, 1385
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42211/annotation1
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://sbols.org/v2#end, 1192
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation1/range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://purl.org/dc/terms/title, Sm/Sp\no\DraIII
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://sbols.org/v2#start, 215
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation1
- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#organism,
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH42211, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/genBankConversion#label, G\to\A
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://sbols.org/v2#start, 2236
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42211/annotation3
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#displayId, pICH42211
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation4/range
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH42211_seq, http://sbols.org/v2#elements, gtggctcttcagtggacgaaagggcctcgtgatacgcctatttttataggttaatgtcatgataataatggtttcttagacgtcaggtggcacttttcggggaaatgtgcgcggaacccctatttgtttatttttctaaatacattcaaatatgtatccgctcatgagacaataaccctgataaatgcttcaataatattgaaaaaggaagagtatgcgctcacgcaactggtccagaaccttgaccgaacgcagcggtggtaacggcgcagtggcggttttcatggcttgttatgactgtttttttggggtacagtctatgcctcgggcatccaagcagcaagcgcgttacgccgtgggtcgatgtttgatgttatggagcagcaacgatgttacgcagcagggcagtcgccctaaaacaaagttaaacatcatgagggaagcggtgatcgccgaagtatcgactcaactatcagaggtagttggcgtcatcgagcgccatctcgaaccgacgttgctggccgtacatttgtacggctccgcagtggatggcggcctgaagccacacagcgatattgatttgctggttacggtgaccgtaaggcttgatgaaacaacgcggcgagctttgatcaacgaccttttggaaacttcggcttcccctggagagagcgagattctccgcgctgtagaagtcaccattgttgtgcacgacgacatcattccgtggcgttatccagctaagcgcgaactgcaatttggagaatggcagcgcaatgacattcttgcaggtatcttcgagccagccacgatcgacattgatctggctatcttgctgacaaaagcaagagaacatagcgttgccttggtaggtccagcggcggaggaactctttgatccggttcctgaacaggatctatttgaggcgctaaatgaaaccttaacgctatggaactcgccgcccgactgggctggcgatgagcgaaatgtagtgcttacgttgtcccgcatttggtacagcgcagtaaccggcaaaatcgcgccgaaggatgtcgctgccgactgggcaatggagcgcctgccggcccagtatcagcccgtcatacttgaagctagacaggcttatcttggacaagaagaagatcgcttggcctcgcgcgcagatcagttggaagaatttgtccattacgtaaaaggcgagatcaccaaggtagtcggcaaataactgtcagaccaagtttactcatatatactttagattgatttaaaacttcatttttaatttaaaaggatctaggtgaagatcctttttgataatctcatgaccaaaatcccttaacgtgagttttcgttccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctttttttctgcgcgtaatctgctgcttgcaaacaaaaaaaccaccgctaccagcggtggtttgtttgccggatcaagagctaccaactctttttccgaaggtaactggcttcagcagagcgcagataccaaatactgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcaccgcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgataagtcgtgtcttaccgggttggactcaagacgatagttaccggataaggcgcagcggtcgggctgaacggggggttcgtgcacacagcccagcttggagcgaacgacctacaccgaactgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaaggcggacaggtatccggtaagcggcagggtcggaacaggagagcgcacgagggagcttccagggggaaacgcctggtatctttatagtcctgtcgggtttcgccacctctgacttgagcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagcaacgcggcctttttacggttcctggccttttgctggccttttgctcacatgttctttcctgcgttatcccctgattctgtggataaccgtattaccgcctttgagtgagctgataccgctcgccgcagccgaacgaccgagcgcagcgagtcagtgagcgaggaagcggaagagcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatcactctgtggtctcaggagagcggagaattaagggagtcacgttatgacccccgccgatgacgcgggacaagccgttttacgtttggaactgacagaaccgcaacgttgaaggagccactcagccgcgggtttctggagtttaatgagctaagcacatacgtcagaaaccattattgcgcgttcaaaagtcgcctaaggtcactatcagctagcaaatatttcttgtcaaaaatgctccactgacgttccataaattcccctcggtatccaattagagtctcatattcactctcatacttgagaccacgaa
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH42211_seq
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42211/annotation1/range, http://sbols.org/v2#start, 1192
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation2
- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- ORIGDB|GenBank
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- VNTDBDATE|516366647|
- LSOWNER|
- VNTNAME|pICH42211|
- VNTAUTHORNAME|Carola Engler|
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- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42211/annotation4/range
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42211/annotation3/range
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42211/annotation0
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://sbols.org/v2#start, 1984
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://purl.org/dc/terms/title, rep\(pMB1)
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH42211/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42211/annotation3/range, http://sbols.org/v2#end, 1999
- http://www.async.ece.utah.edu/pICH42211/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000296
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation4
- http://www.async.ece.utah.edu/pICH42211, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH42211
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://purl.org/dc/terms/title, nos-p
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/genBankConversion#featureType, mutation
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://purl.org/dc/terms/title, G\to\A
- http://www.async.ece.utah.edu/pICH42211_seq, http://sbols.org/v2#displayId, pICH42211_seq
- http://www.async.ece.utah.edu/pICH42211/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://sbols.org/v2#end, 1984
- http://www.async.ece.utah.edu/pICH42211, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42211/annotation2
- http://www.async.ece.utah.edu/pICH42211/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation0/range
- http://www.async.ece.utah.edu/pICH42211_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH42211/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42211/annotation2/range
- http://www.async.ece.utah.edu/pICH42211/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42211/annotation4, http://sbols.org/genBankConversion#label, nos-p
- http://www.async.ece.utah.edu/pICH42211/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42211/annotation1/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42211.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42211.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:35 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:36 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42211.xml
-Python Score = 8
-Java Score = 48
-Number of Files = 74
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH42222.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42222.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH42222_seq, http://sbols.org/v2#elements, caggtggcacttttcggggaaatgtgcgcggaacccctatttgtttatttttctaaatacattcaaatatgtatccgctcatgagacaataaccctgataaatgcttcaataatattgaaaaaggaagagtatgcgctcacgcaactggtccagaaccttgaccgaacgcagcggtggtaacggcgcagtggcggttttcatggcttgttatgactgtttttttggggtacagtctatgcctcgggcatccaagcagcaagcgcgttacgccgtgggtcgatgtttgatgttatggagcagcaacgatgttacgcagcagggcagtcgccctaaaacaaagttaaacatcatgagggaagcggtgatcgccgaagtatcgactcaactatcagaggtagttggcgtcatcgagcgccatctcgaaccgacgttgctggccgtacatttgtacggctccgcagtggatggcggcctgaagccacacagcgatattgatttgctggttacggtgaccgtaaggcttgatgaaacaacgcggcgagctttgatcaacgaccttttggaaacttcggcttcccctggagagagcgagattctccgcgctgtagaagtcaccattgttgtgcacgacgacatcattccgtggcgttatccagctaagcgcgaactgcaatttggagaatggcagcgcaatgacattcttgcaggtatcttcgagccagccacgatcgacattgatctggctatcttgctgacaaaagcaagagaacatagcgttgccttggtaggtccagcggcggaggaactctttgatccggttcctgaacaggatctatttgaggcgctaaatgaaaccttaacgctatggaactcgccgcccgactgggctggcgatgagcgaaatgtagtgcttacgttgtcccgcatttggtacagcgcagtaaccggcaaaatcgcgccgaaggatgtcgctgccgactgggcaatggagcgcctgccggcccagtatcagcccgtcatacttgaagctagacaggcttatcttggacaagaagaagatcgcttggcctcgcgcgcagatcagttggaagaatttgtccattacgtaaaaggcgagatcaccaaggtagtcggcaaataactgtcagaccaagtttactcatatatactttagattgatttaaaacttcatttttaatttaaaaggatctaggtgaagatcctttttgataatctcatgaccaaaatcccttaacgtgagttttcgttccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctttttttctgcgcgtaatctgctgcttgcaaacaaaaaaaccaccgctaccagcggtggtttgtttgccggatcaagagctaccaactctttttccgaaggtaactggcttcagcagagcgcagataccaaatactgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcaccgcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgataagtcgtgtcttaccgggttggactcaagacgatagttaccggataaggcgcagcggtcgggctgaacggggggttcgtgcacacagcccagcttggagcgaacgacctacaccgaactgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaaggcggacaggtatccggtaagcggcagggtcggaacaggagagcgcacgagggagcttccagggggaaacgcctggtatctttatagtcctgtcgggtttcgccacctctgacttgagcgtcgatttttgtgatgctcgtcaggggggcggagcctatggaaaaacgccagcaacgcggcctttttacggttcctggccttttgctggccttttgctcacatgttctttcctgcgttatcccctgattctgtggataaccgtattaccgcctttgagtgagctgataccgctcgccgcagccgaacgaccgagcgcagcgagtcagtgagcgaggaagcggaagagcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaggaaacagctatgaccatgattacgccaagcttgcatgcctgcaggtcgactctagaggatccccggtctcaaatgagcccagaacgacgcccggccgacatccgccgtgccaccgaggcggacatgccggcggtctgcaccatcgtcaaccactacatcgagacaagcacggtcaacttccgtaccgagccgcaggaaccgcaggagtggacggacgacctcgtccgtctgcgggagcgctatccctggctcgtcgccgaggtggacggcgaggtcgccggcatcgcctacgcgggcccctggaaggcacgcaacgcctacgactggacggccgagtcaaccgtgtacgtatccccccgccaccagcggacgggactgggctccacgctctacacccacctgctgaagtccctggaggcacagggcttcaagagcgtggtcgctgtcatcgggctgcccaacgacccgagcgtgcgcatgcacgaggcgctcggatatgccccccgcggcatgctgcgggcggccggcttcaagcacgggaactggcatgacgtgggtttctggcagctggacttcagcctgccggtaccgccccgtccggtcctgcccgtcaccgagatttgagctttgagaccgggtaccgagctcgaattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatggtgcactctcagtacaatctgctctgatgccgcatagttaagccagccccgacacccgccaacacccgctgacgcgccctgacgggcttgtctgctcccggcatccgcttacagacaagctgtgaccatctccgggagctgcatgtgtcagaggttttcaccgtcatcaccgaaacgcgcgagtcgaaagggcctcgtgatacgcctatttttataggttaatgtcatgataataatggtttcttagacgt
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation3/range
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://sbols.org/v2#start, 132
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation4/range
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation0
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://sbols.org/v2#start, 2261
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation7/range
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/genBankConversion#featureType, mutation
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#organism,
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation8/range
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation0/range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH42222_seq
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/genBankConversion#label, P(LAC)
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://purl.org/dc/terms/title, Bar
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://purl.org/dc/terms/title, G\to\A\(Esp3I\removed)
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation8
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/genBankConversion#label, Sm/Sp\no\DraIII
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://purl.org/dc/terms/title, G\to\A
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#source,
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#date, 29-APR-2009
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://sbols.org/v2#start, 3340
- http://www.async.ece.utah.edu/pICH42222_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://purl.org/dc/terms/title, Sm/Sp\no\DraIII
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/genBankConversion#note, lac promoter
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation6
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://sbols.org/v2#end, 2266
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#displayId, pICH42222
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/genBankConversion#featureType, mutation
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://sbols.org/v2#start, 1302
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000296
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://sbols.org/v2#end, 1916
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation5/range
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://sbols.org/v2#start, 1109
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation7
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation3
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://purl.org/dc/terms/title, pUC\seqF
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation0
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation2
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/genBankConversion#label, G\to\A\(Esp3I\removed)
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://sbols.org/v2#end, 2924
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation4
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation0/range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation2/range
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://sbols.org/v2#start, 3284
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://sbols.org/v2#end, 2261
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- VNTDATE|516816006|
- VNTDBDATE|516816006|
- LSOWNER|
- VNTNAME|pICH42222|
- VNTAUTHORNAME|Ernst|
- VNTOAUTHORNAME|Carola Engler|
- VNTOAUTHOREML|engler@icongenetics.de|
- Vector_NTI_Display_Data_(Do_Not_Edit!)
- (SXF
- (CGexDoc "pICH42222" 0 3407
- (CDBMol 0 0 1 1 1 0 0 0 0 "" "" 0 0 0 0 (CObList) (CObList) (CObList)
- (CObList) -1 "")
- (CDocSetData 1 1 0 0 0 0 "MAIN" 1 1 1 1 0 0 1 1 0 1 10 10 4294967295 50 0
- 1 0 (CHomObj 0 0 0 3 75) (CWordArray) (CWordArray)
- (CStringList "ApaLI" "AvaI" "BamHI" "ClaI" "EcoRI" "HindIII" "NcoI"
- "PstI" "SmaI" "XmaI") (CStringList "atg" "gtg")
- (CStringList "taa" "tga" "tag") (CObList) 1 "{(0,1),2}" 0 0 "" 0
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- #190=(CGroupWidget (CWidget 14 (16 0) 1 2 0 0 Nil -322 100)
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- (CSeqView 10 10 (CObjectList) (CObList) 1 (CObList)) (CObList)
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- http://www.async.ece.utah.edu/pICH42222_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/v2#displayId, annotation8
- http://www.async.ece.utah.edu/pICH42222, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://sbols.org/v2#start, 2169
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation2
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://sbols.org/v2#start, 1901
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://purl.org/dc/terms/title, P\lac\prom
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://purl.org/dc/terms/title, A\to\T\(Esp3I\removed)
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation6/range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation3
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://sbols.org/v2#end, 1142
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/genBankConversion#label, pUC\seqF
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://sbols.org/v2#end, 3340
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/genBankConversion#label, Bar
- http://www.async.ece.utah.edu/pICH42222/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation4
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/genBankConversion#featureType, mutation
- http://www.async.ece.utah.edu/pICH42222_seq, http://sbols.org/v2#displayId, pICH42222_seq
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation5/range
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://sbols.org/v2#end, 3284
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://sbols.org/genBankConversion#label, G\to\A
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0001411
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/v2#role, http://identifiers.org/so/SO:0005850
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation7/range
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation3/range
- http://www.async.ece.utah.edu/pICH42222/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222_seq
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://sbols.org/v2#end, 1109
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH42222/annotation8/range, http://sbols.org/v2#start, 2245
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation1
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/genBankConversion#vntifkey, 28
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://sbols.org/genBankConversion#label, P\lac\prom
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation5
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation9
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation1/range
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation8
- http://www.async.ece.utah.edu/pICH42222/annotation3, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://purl.org/dc/terms/title, rep\(pMB1)
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation1/range
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation9/range
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation9/range
- http://www.async.ece.utah.edu/pICH42222, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH42222
- http://www.async.ece.utah.edu/pICH42222/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222/annotation7/range, http://sbols.org/v2#end, 2292
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation1/range, http://sbols.org/v2#end, 1901
- http://www.async.ece.utah.edu/pICH42222/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation7
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/genBankConversion#vntifkey, 30
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation5
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH42222/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://purl.org/dc/terms/title, P(LAC)
- http://www.async.ece.utah.edu/pICH42222/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation8, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation8/range
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation4/range
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation9
- http://www.async.ece.utah.edu/pICH42222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42222/annotation6
- http://www.async.ece.utah.edu/pICH42222/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42222/annotation5, http://sbols.org/genBankConversion#label, A\to\T\(Esp3I\removed)
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42222/annotation2/range
- http://www.async.ece.utah.edu/pICH42222/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42222/annotation2, http://sbols.org/genBankConversion#label, rep\(pMB1)
- http://www.async.ece.utah.edu/pICH42222/annotation9/range, http://sbols.org/v2#start, 2354
- http://www.async.ece.utah.edu/pICH42222/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42222/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation1
- http://www.async.ece.utah.edu/pICH42222/annotation9, http://sbols.org/v2#displayId, annotation9
- http://www.async.ece.utah.edu/pICH42222/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42222/annotation6/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42222.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42222.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:39 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:39 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42222.xml
-Python Score = 8
-Java Score = 49
-Number of Files = 75
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH42760.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42760.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation0
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation0/range
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation0
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH42760_seq, http://sbols.org/v2#displayId, pICH42760_seq
- http://www.async.ece.utah.edu/pICH42760, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH42760
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation5/range
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation0/range
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation6
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation1/range
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#displayId, pICH42760
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation6
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation2/range
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH42760_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760_seq
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH42760, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation1
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation5
- http://www.async.ece.utah.edu/pICH42760, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://sbols.org/v2#end, 2446
- http://www.async.ece.utah.edu/pICH42760/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://purl.org/dc/terms/title, Spm (Zea mays)
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation4/range
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation3/range
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation2
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://sbols.org/genBankConversion#label, Spm (Zea mays)
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation4/range
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation6/range
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation1
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation5/range
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000167
- http://www.async.ece.utah.edu/pICH42760, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation3
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation2
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation5
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation4
- http://www.async.ece.utah.edu/pICH42760_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation2/range
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation4
- http://www.async.ece.utah.edu/pICH42760, http://www.ncbi.nlm.nih.gov/genbank#date, 26-MAR-2009
- http://www.async.ece.utah.edu/pICH42760/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH42760/annotation3
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH42760/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH42760/annotation1/range
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGTCAAAGGAGTGTCAGTTAATTAAAGAGTGTCGGGGCCGACACTCTTAATGGAAGTAAAAGTGTGGGTTTTGCTGCACCGACACTCTTAATTTAAGAGTGTCGGGGTCCCGATGAAACCGACGCTTTTAATTTAAGAGTGTGGGTTTTTCCACACCGACACTCTTATGAATGTTACCCTAAATTCCCCAATCCTA
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760
- http://www.async.ece.utah.edu/pICH42760/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH42760/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH42760, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH42760_seq
- http://www.async.ece.utah.edu/pICH42760, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH42760/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH42760/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation6/range
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH42760/annotation3/range
- http://www.async.ece.utah.edu/pICH42760/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH42760/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH42760/annotation2, http://sbols.org/genBankConversion#label, G to A
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH42760.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42760.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:42 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:43 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH42760.xml
-Python Score = 8
-Java Score = 50
-Number of Files = 76
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH43844.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH43844.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/v2#end, 2449
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation0
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/genBankConversion#position, position0
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation4
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation0
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation2/range
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation2
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation4/range
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation1
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation1
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation4/range
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation1/range
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/genBankConversion#label, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/v2#displayId, range0
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation4
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation5/range
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://purl.org/dc/terms/title, Act2 intron (A. thaliana)
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation6/range0
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation6/range1
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/genBankConversion#multiRangeType, join
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation2
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://purl.org/dc/terms/title, Bar phosphimothricin acetyl transferase (S. hygroscopicus)
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation3
- http://www.async.ece.utah.edu/pICH43844, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH43844
- http://www.async.ece.utah.edu/pICH43844_seq, http://sbols.org/v2#elements, GCTTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAAATGAGCCCAGAACGACGCCCGGCCGACATCCGCCGTGCCACCGAGGCGGACATGCCGGCGGTCTGCACCATCGTCAACCACTACATCGAGACAAGCACGGTCAACTTCCGTACCGAGCCGCAGGAACCGCAGGAGTGGACGGACGACCTCGTCCGTCTGCGGGAGCGCTATCCCTGGCTCGTCGCCGAGGTGGACGGCGAGGTAATAGGAACTTTCTGGATCTACTTTATTTGCTGGATCTCGATCTTGTTTTCTCAATTTCCTTGAGATCTGGAATTCGTTTAATTTGGATCTGTGAACCTCCACTAAATCTTTTGGTTTTACTAGAATCGATCTAAGTTGACCGATCAGTTAGCTCGATTATAGCTACCAGAATTTGGCTTGACCTTGATGGAGAGATCCATGTTCATGTTACCTGGGAAATGATTTGTATATGTGAATTGAAATCTGAACTGTTGAAGTTAGATTGAATCTGAACACTGTCAATGTTAGATTGAATCTGAACACTGTTTAAGGTTAGATGAAGTTTGTGTATAGATTCTTCGAAACTTTAGGATTTGTAGTGTCGTACGTTGAACAGAAAGCTATTTCTGATTCAATCAGGGTTTATTTGACTGTATTGAACTCTTTTTGTGTGTTTGCAGGTCGCCGGCATCGCCTACGCGGGCCCCTGGAAGGCACGCAACGCCTACGACTGGACGGCCGAGTCAACCGTGTACGTATCCCCCCGCCACCAGCGGACGGGACTGGGCTCCACGCTCTACACCCACCTGCTGAAGTCCCTGGAGGCACAGGGCTTCAAGAGCGTGGTCGCTGTCATCGGGCTGCCCAACGACCCGAGCGTGCGCATGCACGAGGCGCTCGGATATGCCCCCCGCGGCATGCTGCGGGCGGCCGGCTTCAAGCACGGGAACTGGCATGACGTGGGTTTCTGGCAGCTGGACTTCAGCCTGCCGGTACCGCCCCGTCCGGTCCTGCCCGTCACCGAGATTTGA
- http://www.async.ece.utah.edu/pICH43844_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844_seq
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation5
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation1/range
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation2/range
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/v2#end, 3243
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/v2#displayId, range1
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation7
- http://www.async.ece.utah.edu/pICH43844/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation6/range0
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation0/range
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation6/range1
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/genBankConversion#position, position1
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://sbols.org/v2#end, 2892
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation0/range
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/genBankConversion#label, Act2 intron (A. thaliana)
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation3
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/genBankConversion#label, Act2int1
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation5/range
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844, http://www.ncbi.nlm.nih.gov/genbank#date, 5-MAY-2009
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation7/range
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/genBankConversion#featureType, Intron
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH43844_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/v2#start, 2249
- http://www.async.ece.utah.edu/pICH43844/annotation6/range0, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/genBankConversion#label, Bar phosphimothricin acetyl transferase (S. hygroscopicus)
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://sbols.org/v2#start, 2450
- http://www.async.ece.utah.edu/pICH43844/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH43844, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH43844_seq
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://sbols.org/genBankConversion#vntifkey, 15
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH43844/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH43844/annotation3/range
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation6
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://purl.org/dc/terms/title, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH43844/annotation6/range1, http://sbols.org/v2#start, 2893
- http://www.async.ece.utah.edu/pICH43844, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation3/range
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation5
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH43844/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH43844_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH43844/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH43844/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH43844/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844/annotation7/range
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH43844
- http://www.async.ece.utah.edu/pICH43844/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#displayId, pICH43844
- http://www.async.ece.utah.edu/pICH43844/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation7
- http://www.async.ece.utah.edu/pICH43844/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844_seq, http://sbols.org/v2#displayId, pICH43844_seq
- http://www.async.ece.utah.edu/pICH43844/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH43844, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH43844/annotation6
- http://www.async.ece.utah.edu/pICH43844/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH43844/annotation0, http://sbols.org/v2#displayId, annotation0
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH43844.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH43844.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:45 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:46 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH43844.xml
-Python Score = 8
-Java Score = 51
-Number of Files = 77
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44022.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44022.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44022, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation5
- http://www.async.ece.utah.edu/pICH44022_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022_seq, http://sbols.org/v2#elements, GCTTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAAATGGAACGAGCTATACAAGGAAACGATGCTAGGGAACAAGCTTATGGTGAACGTTGGAATGGAGGATCAGGAAGTTCCACTTCTCCCTTCAAACTTCCTGACGAAAGTCCGAGTTGGACTGAGTGGCGGCTACATAACGATGAGACTATTTCGAATCAAGATAATCCCCTTGGTTTCAAGGAAAGCTGGGGTTTCGGGAAAGTTGTATTTAAGAGATATCTCAGATACGACGGGACGGAAACTTCACTGCACAGAGTCCTTGGATCTTGGACGGGAGATTCGGTTAACTATGCAGCATCTCGATTTCTCGGTTTCGACCAGATCGGATGTACCTATAGTATTCGGTTTCGAGGAGTTAGTGTCACCATTTCTGGAGGGTCGCGAACTCTTCAGCATCTCAGTGAAATGGCAATTCGGTCTAAGCAAGAACTGCTACAGCTTACCCCAGTCAAAGTGGAAAGTGATGTATCAAGAGGATGCCCTGAAGGTGTTGAAACCTTCGAAGAAGAAAGCGAGTAA
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation2/range
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation6/range
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44022_seq
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://sbols.org/v2#end, 2767
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation3/range
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation4/range
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation4
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/genBankConversion#label, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation5/range
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation6
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://sbols.org/v2#start, 2249
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation6/range
- http://www.async.ece.utah.edu/pICH44022, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44022
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation3/range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation0/range
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://purl.org/dc/terms/title, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44022, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation1
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation0
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation1/range
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation4/range
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation4
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://purl.org/dc/terms/title, P19 (TBSV)
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/genBankConversion#label, P19 (no Esp3I)
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44022/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022
- http://www.async.ece.utah.edu/pICH44022/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#displayId, pICH44022
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation2
- http://www.async.ece.utah.edu/pICH44022, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44022_seq, http://sbols.org/v2#displayId, pICH44022_seq
- http://www.async.ece.utah.edu/pICH44022_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022_seq
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation6
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44022, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44022/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation0
- http://www.async.ece.utah.edu/pICH44022/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation3
- http://www.async.ece.utah.edu/pICH44022/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44022/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44022/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation3
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation1
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44022, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44022/annotation5
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://sbols.org/genBankConversion#label, P19 (TBSV)
- http://www.async.ece.utah.edu/pICH44022, http://www.ncbi.nlm.nih.gov/genbank#date, 27-MAY-2009
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation1/range
- http://www.async.ece.utah.edu/pICH44022/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44022/annotation2
- http://www.async.ece.utah.edu/pICH44022/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44022/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44022/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation2/range
- http://www.async.ece.utah.edu/pICH44022/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation5/range
- http://www.async.ece.utah.edu/pICH44022/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44022/annotation0/range
- http://www.async.ece.utah.edu/pICH44022_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44022/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44022.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44022.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:49 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44022.xml
-Python Score = 8
-Java Score = 52
-Number of Files = 78
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44157.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44157.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation1
- http://www.async.ece.utah.edu/pICH44157, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44157, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation6
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44157_seq
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/genBankConversion#label, AtRbcS native start of transcription
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGCTTAAGTGGGCCGTAAGTGCAATTGCGTTGTGCTCCAAAAGGAACGGTGCCGTGGGTTCCTCTTGTTCATCAGAAATATATTAATTAGCCGTAAAACCTGAAAATTCACAAGCATTTGGATTGTTTTCTAATTTAATATCCATTATGTGACTAAAAGTTCTAGTGATCGTACATACTACATAGAAAATAATAACACAAAATACTAGTTTACATTTCCCAATTAAAAACCATTTTGAATGAACTCTGTCTGATTTAATTATACTTTTAAAATGTGGGATGAATTCAAAGATTATACTTATATTCTTATTATTTAAGATTATCAAGTGGAAAAATAAAAATATGAATGTGTTAATATAAGGTAATAGAAATTTAATCATTTTTTTAATCTATATGTAAAAAGTATTTAACCGATATCTACAATTTGACGCCTCCCAATTGAAAGGAGCCAAAAGCAACCGATCAAGTGCAGACCAGTAGCCATACACATTCACTCCTACCCTTACATGAGAAAGATAAGATTATGGAGTTTTCTGCCACGTGATCTTATCCTAGTGGTCCAAATCGATAAGGGTGTCAACACCTTTCCTTAATCCTGTGGCAATTAACGACGTTATCATGAATTATGGCCCCTTTGATCATTAGGGCTAGTTGCCTCTAGCGGTTCCCACTATATAAAGATGACAAAACCAACAGA
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation4
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation2
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation4
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://purl.org/dc/terms/title, AtRbcS native start of transcription
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44157, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation2/range
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://sbols.org/v2#end, 2946
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation2
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation0/range
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation1/range
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation3/range
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44157, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44157
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation0
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation5
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation5/range
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation6
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation0/range
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation6/range
- http://www.async.ece.utah.edu/pICH44157_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation3
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation6/range
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation4/range
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation5
- http://www.async.ece.utah.edu/pICH44157_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation7/range
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation3
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation7/range
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation4/range
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation7
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44157, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://sbols.org/v2#start, 2946
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation1/range
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157_seq, http://sbols.org/v2#displayId, pICH44157_seq
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://sbols.org/v2#end, 2946
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation7
- http://www.async.ece.utah.edu/pICH44157/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44157/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44157/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157_seq
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation0
- http://www.async.ece.utah.edu/pICH44157/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44157/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation5/range
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44157, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/genBankConversion#label, AtRbcS2B
- http://www.async.ece.utah.edu/pICH44157/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#displayId, pICH44157
- http://www.async.ece.utah.edu/pICH44157/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44157/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44157/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44157/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44157/annotation3/range
- http://www.async.ece.utah.edu/pICH44157/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44157/annotation2/range
- http://www.async.ece.utah.edu/pICH44157, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44157/annotation1
- http://www.async.ece.utah.edu/pICH44157/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44157/annotation6, http://purl.org/dc/terms/title, AtRbcS2B
- http://www.async.ece.utah.edu/pICH44157/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44157.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44157.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:52 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:53 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44157.xml
-Python Score = 8
-Java Score = 53
-Number of Files = 79
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44179.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44179.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44179, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation5/range
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation2/range
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44179, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation1/range
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation6
- http://www.async.ece.utah.edu/pICH44179_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179_seq
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation1/range
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation1
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation4
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation5
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation3/range
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation4/range
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation4
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation1
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation5/range
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation3
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTACAAACAAGTAAGTAAGAGAAAAACCAAAAGAAGAAGAGAAACAACAAGAAGAAGT
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation4/range
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://purl.org/dc/terms/title, AtRbcS2B 5'UTR
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation0
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/genBankConversion#label, AtRbcS2B 5'UTR
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation2/range
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation3
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#displayId, pICH44179
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44179, http://www.ncbi.nlm.nih.gov/genbank#date, 2-JUN-2009
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation2
- http://www.async.ece.utah.edu/pICH44179_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation6/range
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation6
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation2
- http://www.async.ece.utah.edu/pICH44179/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation3/range
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation0/range
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://sbols.org/v2#end, 2307
- http://www.async.ece.utah.edu/pICH44179, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44179
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation0
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44179/annotation6/range
- http://www.async.ece.utah.edu/pICH44179/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44179_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44179/annotation5
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44179/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44179_seq
- http://www.async.ece.utah.edu/pICH44179/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44179/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44179, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44179, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44179/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44179_seq, http://sbols.org/v2#displayId, pICH44179_seq
- http://www.async.ece.utah.edu/pICH44179/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44179/annotation0/range
- http://www.async.ece.utah.edu/pICH44179/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44179/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44179/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44179/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44179.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44179.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:55 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:56 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44179.xml
-Python Score = 8
-Java Score = 54
-Number of Files = 80
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44188.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44188.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44188_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44188, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation0
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation6
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation4
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://purl.org/dc/terms/title, BSMH 5'UTR
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://purl.org/dc/terms/title, TACT
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation1/range
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation3/range
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation2
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://purl.org/dc/terms/title, AATG
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44188, http://www.ncbi.nlm.nih.gov/genbank#date, 2-JUN-2009
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation3/range
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation3
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation3
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/genBankConversion#label, BSMH 5'UTR
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation1
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation0/range
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation4/range
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation1/range
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation5/range
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188_seq
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation5
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44188, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation5
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#displayId, pICH44188
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation2/range
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44188/annotation6
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation6/range
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation2
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation6/range
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44188_seq
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation0
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation4/range
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44188/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44188, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation5/range
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH44188_seq, http://sbols.org/v2#displayId, pICH44188_seq
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation4
- http://www.async.ece.utah.edu/pICH44188/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44188/annotation0/range
- http://www.async.ece.utah.edu/pICH44188_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTAAAAGAAAAGGAACAACCCTGTTGTTGTTCGACGCTATACTAAATATATATTATCTTATTAGTGCATTTCTTTTACCGCTTCACAG
- http://www.async.ece.utah.edu/pICH44188_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44188/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://sbols.org/v2#end, 2339
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44188/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44188/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/genBankConversion#label, TACT
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation1
- http://www.async.ece.utah.edu/pICH44188, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44188
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/genBankConversion#label, AATG
- http://www.async.ece.utah.edu/pICH44188/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44188/annotation2/range
- http://www.async.ece.utah.edu/pICH44188/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44188/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44188/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44188/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44188/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44188/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44188.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44188.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:20:59 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:00 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44188.xml
-Python Score = 8
-Java Score = 55
-Number of Files = 81
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44199.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44199.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44199, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation0/range
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation6
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation6/range
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation3
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44199_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTACACCACCAACACAACCAAACCCACCACGCCCAATTGTTACACACCCGCTTGGAAAAGCAAGTCTAACAA
- http://www.async.ece.utah.edu/pICH44199, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation1/range
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44199_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199_seq
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation1/range
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44199_seq, http://sbols.org/v2#displayId, pICH44199_seq
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44199, http://www.ncbi.nlm.nih.gov/genbank#date, 2-JUN-2009
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation5/range
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation4/range
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/genBankConversion#label, PVX 5'UTR
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44199_seq
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#displayId, pICH44199
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation5
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation4/range
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation2
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation0
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation2/range
- http://www.async.ece.utah.edu/pICH44199, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation2/range
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44199/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation3
- http://www.async.ece.utah.edu/pICH44199_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation3/range
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44199, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44199
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation3/range
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://sbols.org/v2#end, 2321
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation1
- http://www.async.ece.utah.edu/pICH44199/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation0/range
- http://www.async.ece.utah.edu/pICH44199_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://purl.org/dc/terms/title, PVX 5'UTR
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation5/range
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation5
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation4
- http://www.async.ece.utah.edu/pICH44199/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44199/annotation6/range
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation4
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44199/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation1
- http://www.async.ece.utah.edu/pICH44199/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation2
- http://www.async.ece.utah.edu/pICH44199/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44199, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44199/annotation0
- http://www.async.ece.utah.edu/pICH44199/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44199/annotation5, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH44199/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44199/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44199/annotation6
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44199/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH44199/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44199/annotation0/range, http://sbols.org/v2#end, 4
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44199.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44199.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:03 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:04 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44199.xml
-Python Score = 8
-Java Score = 56
-Number of Files = 82
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44222.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44222.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation0/range
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation2
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/genBankConversion#label, AATG
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation1/range
- http://www.async.ece.utah.edu/pICH44222, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/genBankConversion#label, TACT
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44222_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation0
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://purl.org/dc/terms/title, AATG
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation2/range
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44222_seq
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://purl.org/dc/terms/title, TACT
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation6/range
- http://www.async.ece.utah.edu/pICH44222, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation6
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#displayId, pICH44222
- http://www.async.ece.utah.edu/pICH44222_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTTTATTTACAAGAGCGTACGGTTCAATCCCTGCCTCCCCTGTAAAACTACCCTTTGAAAACCTCTCTTTCTTAATCTTTTCTTTGTAATTCC
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation5
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44222, http://www.ncbi.nlm.nih.gov/genbank#date, 2-JUN-2009
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation4/range
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation6/range
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222_seq, http://sbols.org/v2#displayId, pICH44222_seq
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation3/range
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation4
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation4/range
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation1/range
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/genBankConversion#label, CMV1 5'UTR
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation0
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation3
- http://www.async.ece.utah.edu/pICH44222, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://purl.org/dc/terms/title, CMV1 5'UTR
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation4
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation0/range
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation1
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44222/annotation5
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44222, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44222
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44222, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44222/annotation5/range
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation3/range
- http://www.async.ece.utah.edu/pICH44222/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation2/range
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44222/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation1
- http://www.async.ece.utah.edu/pICH44222/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation5/range
- http://www.async.ece.utah.edu/pICH44222/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation3
- http://www.async.ece.utah.edu/pICH44222/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222
- http://www.async.ece.utah.edu/pICH44222_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222_seq
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44222/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation2
- http://www.async.ece.utah.edu/pICH44222/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44222/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44222/annotation6
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44222/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44222/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44222/annotation6/range, http://sbols.org/v2#end, 2344
- http://www.async.ece.utah.edu/pICH44222/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44222.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44222.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:06 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:07 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44222.xml
-Python Score = 8
-Java Score = 57
-Number of Files = 83
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44233.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44233.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation2
- http://www.async.ece.utah.edu/pICH44233_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCATACTGTTTATTTACAAGAGCGTACGGTTCAACCCCTGCCTCCCCTGTAAAACTCCCTAGACTTAAATCTTTTCTTTCTAGTATCTTTTC
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation6
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44233_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233_seq
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation5
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/genBankConversion#label, TACT
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44233_seq
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation6
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation2/range
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation4
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation3
- http://www.async.ece.utah.edu/pICH44233, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation4/range
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://purl.org/dc/terms/title, AATG
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation3
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation6/range
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation5/range
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation3/range
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation0
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation6/range
- http://www.async.ece.utah.edu/pICH44233, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44233
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://purl.org/dc/terms/title, TACT
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation1/range
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation4
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation5/range
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation0/range
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation3/range
- http://www.async.ece.utah.edu/pICH44233, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44233, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation2
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation0/range
- http://www.async.ece.utah.edu/pICH44233_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation1
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation1
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation5
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44233/annotation0
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233/annotation1/range
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation2/range
- http://www.async.ece.utah.edu/pICH44233/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://purl.org/dc/terms/title, CMV2 5'UTR
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44233
- http://www.async.ece.utah.edu/pICH44233, http://www.ncbi.nlm.nih.gov/genbank#date, 2-JUN-2009
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#displayId, pICH44233
- http://www.async.ece.utah.edu/pICH44233/annotation6, http://sbols.org/genBankConversion#label, CMV2 5'UTR
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH44233_seq, http://sbols.org/v2#displayId, pICH44233_seq
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44233/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44233/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44233/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation0, http://sbols.org/genBankConversion#label, AATG
- http://www.async.ece.utah.edu/pICH44233/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44233/annotation4/range
- http://www.async.ece.utah.edu/pICH44233/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44233, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44233/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation6/range, http://sbols.org/v2#end, 2336
- http://www.async.ece.utah.edu/pICH44233/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44233/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44233/annotation0/range, http://sbols.org/v2#displayId, range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44233.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44233.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:10 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:11 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44233.xml
-Python Score = 8
-Java Score = 58
-Number of Files = 84
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH44300.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44300.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH44300, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation2/range
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation5
- http://www.async.ece.utah.edu/pICH44300_seq, http://sbols.org/v2#elements, CGCTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGCTTGCTCTCAAGATCAAAGGCTTAAAAAGCTGGGGTTTTATGAATGGGATCAAAGTTTCTTTTTTTCTTTTATATTTGCTTCTCCATTTGTTTGTTTCATTTCCCTTTTTGTTTTCGTTTCTATGATGCACTTGTGTGTGACAAACTCTCTGGGTTTTTACTTACGTCTGCGTTTCAAAAAAAAAAACCGCTTTCGTTTTGCGTTTTAGTCCCATTGTTTTGTAGCTCTGAGTGATCGAATTGATGCCTCTTTATTCCTTTTGTTCCCTATAATTTCTTTCAAAACTCAGAAGAAAAACCTTGAAACTCTTTGCAATGTTAATATAAGTATTGTATAAGATTTTTATTGATTTGGTTATTAGTCTTACTTTTGCTACCTCCATCTTCACTTGGAACTGATATTCTGAATAGTTAAAGCGTTACATGTGTTCCATTCACAAATGAACTTAAACTAGCACAAAGTCAGATATTTTAAGATCGCACCATTT
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation6/range
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation3
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://purl.org/dc/terms/title, CGCT 4bp overhang
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/genBankConversion#label, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation3/range
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://sbols.org/v2#end, 2736
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation5/range
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH44300_seq
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation4
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation3/range
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://purl.org/dc/terms/title, ATact2 terminTOR
- http://www.async.ece.utah.edu/pICH44300, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/genBankConversion#featureType, MIsc._Feature
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation0
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation0
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/genBankConversion#label, CGCT 4bp overhang
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation6
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation0/range
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation2/range
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/genBankConversion#featureType, MIsc._Feature
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation0/range
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation2
- http://www.async.ece.utah.edu/pICH44300_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300_seq
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/genBankConversion#label, A.t. act2 ter
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation6/range
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation1
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation4/range
- http://www.async.ece.utah.edu/pICH44300, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH44300, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation4
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#displayId, pICH44300
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://purl.org/dc/terms/title, GCTT 4bp overhang
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation2
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation6
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH44300/annotation1/range
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH44300_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH44300/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/genBankConversion#label, ATact2 terminTOR
- http://www.async.ece.utah.edu/pICH44300_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH44300_seq, http://sbols.org/v2#displayId, pICH44300_seq
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation3
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation1
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH44300/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation1/range
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation5/range
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/genBankConversion#vntifkey, 43
- http://www.async.ece.utah.edu/pICH44300, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH44300
- http://www.async.ece.utah.edu/pICH44300/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH44300/annotation4/range
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://sbols.org/genBankConversion#featureType, Terminator
- http://www.async.ece.utah.edu/pICH44300/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH44300/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH44300/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH44300, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH44300/annotation5
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH44300/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH44300/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH44300/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH44300/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH44300/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH44300.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44300.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:14 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:15 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH44300.xml
-Python Score = 8
-Java Score = 59
-Number of Files = 85
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45089.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45089.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation2/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation4/range
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation4
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation2
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation1
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45089_1_seq
- http://www.async.ece.utah.edu/pICH45089_1, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45089_1, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation1/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation0/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/genBankConversion#label, 2x35S pro
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation6/range
- http://www.async.ece.utah.edu/pICH45089_1_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45089_1_seq, http://sbols.org/v2#displayId, pICH45089_1_seq
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#displayId, pICH45089_1
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation5
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation4
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation2
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation3
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation7/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://sbols.org/v2#end, 3004
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation5/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation7/range
- http://www.async.ece.utah.edu/pICH45089_1_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGTCAACATGGTGGAGCACGACACTCTGGTCTACTCCAAAAATGTCAAAGATACAGTCTCAGAAGATCAAAGGGCTATTGAGACTTTTCAACAAAGGATAATTTCGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAGTAGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCATTCAAGATCTCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGAGGTTCCAACCACGTCTACAAAGCAAGTGGATTGATGTGATAACATGGTGGAGCACGACACTCTGGTCTACTCCAAAAATGTCAAAGATACAGTCTCAGAAGATCAAAGGGCTATTGAGACTTTTCAACAAAGGATAATTTCGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAGTAGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCATTCAAGATCTCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGAGGTTCCAACCACGTCTACAAAGCAAGTGGATTGATGTGACATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACACGC
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45089_1_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1_seq
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/genBankConversion#label, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation6
- http://www.async.ece.utah.edu/pICH45089_1, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45089_1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45089_1, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation5
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation7
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation6
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation0
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://purl.org/dc/terms/title, 2x35S pro
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation5/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/genBankConversion#label, CaMV 35s 5'UT
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation1
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://sbols.org/v2#end, 3004
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation7
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation0
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation3/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation0/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation4/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation6/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://sbols.org/v2#start, 2998
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45089_1/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://purl.org/dc/terms/title, CaMV 35s 5'UT
- http://www.async.ece.utah.edu/pICH45089_1, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45089-1
- http://www.async.ece.utah.edu/pICH45089_1_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45089_1/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH45089_1/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45089_1/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45089_1/annotation2/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://purl.org/dc/terms/title, TACT 4bp overhang
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation3/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45089_1/annotation1/range
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45089_1/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45089_1/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45089_1/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45089_1/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45089_1/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45089_1/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45089_1/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45089_1/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45089_1/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45089_1/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45089_1, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45089_1/annotation3
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45089.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45089.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:18 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:19 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45089.xml
-Python Score = 8
-Java Score = 60
-Number of Files = 86
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45125.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45125.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation3/range
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation2/range
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation1/range
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation3
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation1
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/genBankConversion#label, LHB1B1 pro
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45125_seq, http://sbols.org/v2#displayId, pICH45125_seq
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#displayId, pICH45125
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation0/range
- http://www.async.ece.utah.edu/pICH45125, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation6
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation2
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation4
- http://www.async.ece.utah.edu/pICH45125, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation2/range
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://sbols.org/v2#end, 2881
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation0
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation3
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45125_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125_seq
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45125, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45125, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation6/range
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45125_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGATATGACTGGTAAGTTTTTCTTGCCAATACGAATTAGAAAACATGTCTTTGAAGATGAACTGTATTTTTTTTTTTTACTTTGTTGTCATTTTAATGTACTTTCTTATCAGGATTAAATCTTCTGTAATTTAGAGTAGTTTTTTTAACAAGATAATTAACAAACTTAGAGTAATGAAAATTGAGATGTTCAGTTTTCACTCATATTTCACATTTTGGTGAAAGAGTGGGTAGTATGCAACGTTCTAAGTATGTTTGGACTTTGTATCATGTTGTTTTGATTCTTTGACGACATGTCTATTTGGGAAACACCAATGACGTGTACCTTGAGACTGATACGATTCAAAGGGATAGAAACACGTCAGATTTACAAGTGGCACCTCTTCAATGGACAATGGGTATTCCAATATGCTAAGATGCTACGAGATATCTAATTTATCTAACACAACTCAATTCCAAACCAAAAATCTGATGCCAGCTCGACAAGACAAAAAATCTAAGCTCAAAAATGTCAACAACCAATAGAAATCAAGGCATTGACGATATCACGAGATAAGCAAATTAAATCTTCAAGTTTTGCAATTCATATGTACGTTATAAATACCCAAAAACCTCACCGTAACCTAGCTATCC
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation4/range
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation5
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation4/range
- http://www.async.ece.utah.edu/pICH45125/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation0
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation5/range
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation6/range
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation3/range
- http://www.async.ece.utah.edu/pICH45125/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45125_seq
- http://www.async.ece.utah.edu/pICH45125/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45125/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation2
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation4
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://purl.org/dc/terms/title, LHB1B1 pro
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation5
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation1
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45125/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45125/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45125/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45125/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation5/range
- http://www.async.ece.utah.edu/pICH45125/annotation0, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45125/annotation6
- http://www.async.ece.utah.edu/pICH45125, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45125
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45125, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45125/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45125/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45125/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45125/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45125/annotation0/range
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45125/annotation1/range
- http://www.async.ece.utah.edu/pICH45125_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45125/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45125.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45125.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:22 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:23 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45125.xml
-Python Score = 8
-Java Score = 61
-Number of Files = 87
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45131.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45131.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45131, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45131, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45131
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45131_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation6
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation6
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation4
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation4/range
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation1
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45131_seq, http://sbols.org/v2#displayId, pICH45131_seq
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation0
- http://www.async.ece.utah.edu/pICH45131_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131_seq
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45131_seq
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation5
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation1/range
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation1
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation0
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation4/range
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation2
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://purl.org/dc/terms/title, LHB1B2 pro
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation3
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation5/range
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation6/range
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45131, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGTTGTTGCCGAAAACATTCAACAAAATCAATCAAAGGTATCAGTTAATATCATTGTCGACGGTTTTATATTATTAACTTATGATCGTAAGAACTTCGTATCACTTTTTGTTTCATCTAACTGCATTGTTTTACATAACATTGATATATATTTGTTTGGTAAGTGTTTCTAGTTTCACTTAAAAACTTTGTAGTTTGGCGTTCGAAACAAACTTGATAAGAAAAAAAAGAAAATATTATTGAGAGCATGAAGTGGATTGGAATTAAAGAAAACAAGGAAAAAGAAAAAAATAGATTGGAATAATTTCAAATATTTCTTTCCAATAATTCAAGCATTTATCTTTGAAAATTTCCCCAAAGTTTCTTTGTGTACAAATGACAAGTGTTTTCGTTGCAGCTAAAGAATCTAGCAAAAGCTTATGGACTAGAGAGTGACACATAGGACAAGATAACGACAATCCCAAAATCTCATAAGCCAATCACTAAACAGATACAGATACTTCACAGATAACAAACCTTACTCTTAACATTGCTATAAAGTGGACGTATACCCCAACCATTTTCAA
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation0/range
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation2/range
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation0/range
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45131/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation3/range
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation3
- http://www.async.ece.utah.edu/pICH45131_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45131, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#displayId, pICH45131
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation6/range
- http://www.async.ece.utah.edu/pICH45131/annotation0, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation2
- http://www.async.ece.utah.edu/pICH45131/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://sbols.org/v2#end, 2814
- http://www.async.ece.utah.edu/pICH45131/annotation6, http://sbols.org/genBankConversion#label, LHB1B2 pro
- http://www.async.ece.utah.edu/pICH45131/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45131/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation5/range
- http://www.async.ece.utah.edu/pICH45131/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131/annotation2/range
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation4
- http://www.async.ece.utah.edu/pICH45131, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45131/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45131/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45131/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation3/range
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45131/annotation5
- http://www.async.ece.utah.edu/pICH45131, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45131
- http://www.async.ece.utah.edu/pICH45131, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45131/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45131/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45131/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45131/annotation1/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45131.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45131.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:27 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:28 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45131.xml
-Python Score = 8
-Java Score = 62
-Number of Files = 88
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45152.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45152.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45152, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45152
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation4/range
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://purl.org/dc/terms/title, CAB1 pro
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45152, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation0/range
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation2/range
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45152_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGTTTCCGGTTGAAATGGGTTTGGTGAATATCCGGTTCAGTTATATGGTGGCCGTTGGAATTGGCTTATTAGTTGTGGCCGTTGTTGAAGCCGTTGGTATTGGTAAGGGAGAAGCAGACTTGTGGCTATGAGTCTATGACCATGACTCGTGATTATGGAGCTGTCTTATGACCCTGACCATCACCTTGATCTGGTGGATTCCAATGTTTTCTTCTTCTTCTAATAAAATATTATGGTCAATACAGGTGCTAATTAAGATGGTAATAATTTCTTATGTTTCTGTGGTAAAGTTTGATTCAATTCCGTAGTTTTAGATAATCTTATTTCCATACATAAATTTTATAGTTTTATCTACTTTGTTCTTATGTTTTATCTCTAGCCAAGAGTTATTATTATTATCAGAAGAAGAAAAAAAAAAGAAGCATATATACAAAAGGTTTAATAAAATGTATTATACAAGGCAATTATCCAAATTTTTTTTGTTTTGGTTTACATTGATGCTCTCAGGATTTCATAAGGATAGAGAGATCTATTCGTATACGTGTCACGTCATGAGTGGGTGTTTCGCCAATCCATGAAACGCACCTAGATATCTAAAACACATATCAATTGCGAATCTGCGAAGTGCGAGCCATTAACCACGTAAGCAAACAAACAATCTAAACCCCAAAAAAAATCTATGACTAGCCAATAGCAACCTCAGAGATTGATATTTCAAGATAAGACAGTATTTAGATTTCTGTATTATATATAGCGAAAATCGCATCAATACCAAACCACC
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation0/range
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation0
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation5
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45152, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation3
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45152_seq
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation3/range
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation1
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45152_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation5/range
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation3/range
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#displayId, pICH45152
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation6
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation2
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation1/range
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation4
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation2/range
- http://www.async.ece.utah.edu/pICH45152_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152_seq
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation2
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation1
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation4
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45152/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/genBankConversion#label, CAB1 pro
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45152/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation5/range
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation1/range
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation6/range
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45152/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45152/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45152/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation6
- http://www.async.ece.utah.edu/pICH45152/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45152/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45152/annotation6/range, http://sbols.org/v2#end, 3030
- http://www.async.ece.utah.edu/pICH45152, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45152/annotation3
- http://www.async.ece.utah.edu/pICH45152/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation5
- http://www.async.ece.utah.edu/pICH45152/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation4/range
- http://www.async.ece.utah.edu/pICH45152, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45152/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45152/annotation0
- http://www.async.ece.utah.edu/pICH45152_seq, http://sbols.org/v2#displayId, pICH45152_seq
- http://www.async.ece.utah.edu/pICH45152/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45152/annotation6/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45152.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45152.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:31 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:32 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45152.xml
-Python Score = 8
-Java Score = 63
-Number of Files = 89
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45173.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45173.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45173_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation2/range
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation1/range
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45173_seq, http://sbols.org/v2#displayId, pICH45173_seq
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45173, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGCGGGCTTGATTCGATATTAATATGGGATGGTGTACAACGGGTGAAATTTTAGAATTGACTGGTTTGAGTTGATAATAATTTGCGATAGAACTAGGAGTGAAATCCTAGAATGACAATCAAGTTATTATTATACAATTAAATACTACCACAGGTGAAATCCTAGAATTGACGGGTTTGATTCGATATTAATATGGGATGGTGTACTACGGGTGAAATCCGAGAAACAACAATCAAAATACAATTATACAATATTAAACATTTAACAAAATAAACAAATACAACTTAAAACTTTAAAATTTGAGTTATAAAATTTTGTCTCGCGGTGAATTATACATTTAAATCAAACAATAGCAGAAATTTATTAAGTCATCCTAAGAAATATTCAATTATTTTTTATTTAATGAAAATATAGACCCGCGGTATACCGCGGATTAATATTTAGTGCTATTGATAAATTTATCTCAACGTTCAGCTTTGACATTGTGAAATGCATTATGAGTCATGACTCTGTTTATAGATATTCCTGTTATAGTATTTATTAACCGAAGTAATGTAAACCAAATTTTAAAAATACATACAAGATAAATAAAAGGTCCAAAACATTATATTTACGGTCATGCATCTGATTTCTTTTCTTCCAAAAGGAAGGAGCCAAAGCAACCGATCAAGTGGAGACTAGTAAACCATACACAATCACTCATTTCCTCACAAAAGAAAGATAAGATAAGGGTGTCAACACCTTTCCTTAATCATGTGGTAGTGAACGAGTTATCATGAATCCCGGACCCTTTGATCATTA
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation5/range
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation0
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/genBankConversion#label, RbcS1B
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#displayId, pICH45173
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation2/range
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://purl.org/dc/terms/title, RbcS1B
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation6
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation4/range
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation3
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation3/range
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://sbols.org/v2#end, 3050
- http://www.async.ece.utah.edu/pICH45173, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45173, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45173_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173_seq
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation5
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45173, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45173
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation0/range
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation0/range
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45173_seq
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation6/range
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation4/range
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation3/range
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation3
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation5/range
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation1
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45173/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45173/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation0
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation4
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45173/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation1/range
- http://www.async.ece.utah.edu/pICH45173/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45173/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45173/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45173/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation5
- http://www.async.ece.utah.edu/pICH45173/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation1
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation2
- http://www.async.ece.utah.edu/pICH45173/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation2
- http://www.async.ece.utah.edu/pICH45173/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45173/annotation6/range
- http://www.async.ece.utah.edu/pICH45173/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45173, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45173/annotation6
- http://www.async.ece.utah.edu/pICH45173/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45173/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45173/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45173, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45173/annotation4
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45173.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45173.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:34 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:35 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45173.xml
-Python Score = 8
-Java Score = 64
-Number of Files = 90
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45180.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45180.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation5
- http://www.async.ece.utah.edu/pICH45180, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45180_seq, http://sbols.org/v2#elements, TACTTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGTTAGAATTCTTTTGATAGGTTTACTTCCATTAGTCTGAAATGGAATCTTATTTATAAGTCTGCCTGAAAAATCTTAACAATTGATATTAATAAAACGGAAAGAGTAATGAATATTTTTAAGAGCATCTCGAATCTATCTCTATTTTTATTTATATACTCTATTTTTGTATTTATTTAACTCTAACTCATCTCTATTTTCATTTGTAAAATAGAAATTTCTAATTTTTTTTCTAAAGCAAAAAATAGAGATTTTTATTTTTTCTCTTATTTATTTTTTCTAACGAATTTTTGAGGAACCATTGAAGTTAAAATATAAATCTCTATTATATTTTTTCCTCTATATTCAGAAAGAAAATAATAGAAACAAATATTGGAGATGGTTAAAGCTTTTTTTTTTGTCCGGATAAATATCATACAATATATTTATGTAAATATCAAATTTAAATAATTTTGTTATAACTATTTTTTAATGCGACCTTATTTCCAAAGAAAGTGTTAAGCCAAATTAAATCATACATGGTAAATAAGAGGTCCAAAAGACCAAAAGCATTAAATTTAAGGTAATGCGTCTGGTTTCTTTTCTCCCAAACGAAAGGAGCCAAAAGCAACCGATCAAGTGCAGACCAGTAACCGCACATTCACTTCATTTCCCCCACAAGAGAAAAGATAAGATAATGGAGTTTTCTGCCACGTGGCCTTATCCTAGTGGTGCGTACCGATAAGGGTGTCAACACCTTTCCTTAATCCTGTGGCAGTAAACGACGTTATCATGAATCATGGACCCTTTGATCATGAGGGC
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/genBankConversion#label, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation6
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45180
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://sbols.org/v2#end, 3051
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation6/range
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation4/range
- http://www.async.ece.utah.edu/pICH45180_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/genBankConversion#label, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation5/range
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45180_seq
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://purl.org/dc/terms/title, TACT 4 bp overhang
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation1
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation4
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation0
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation0
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180_seq, http://sbols.org/v2#displayId, pICH45180_seq
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://purl.org/dc/terms/title, GGAG 4 bp overhang
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#displayId, pICH45180
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation4/range
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45180, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation5/range
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45180_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation2
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation2/range
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation2/range
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation6
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation4
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation3
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45180, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation1/range
- http://www.async.ece.utah.edu/pICH45180/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation3/range
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation5
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation1
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation3/range
- http://www.async.ece.utah.edu/pICH45180/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45180/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation0/range
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://sbols.org/genBankConversion#label, Rbcs 3B pro
- http://www.async.ece.utah.edu/pICH45180/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45180/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45180/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45180/annotation6, http://purl.org/dc/terms/title, Rbcs 3B pro
- http://www.async.ece.utah.edu/pICH45180/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation2
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45180/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45180/annotation0/range
- http://www.async.ece.utah.edu/pICH45180/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation6/range
- http://www.async.ece.utah.edu/pICH45180, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45180/annotation3
- http://www.async.ece.utah.edu/pICH45180_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180_seq
- http://www.async.ece.utah.edu/pICH45180/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45180/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45180/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45180/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45180/annotation1/range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45180.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45180.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:38 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:39 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45180.xml
-Python Score = 8
-Java Score = 65
-Number of Files = 91
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45195.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45195.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation0
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation0/range
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation1
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation7/range
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#displayId, pICH45195
- http://www.async.ece.utah.edu/pICH45195_seq, http://sbols.org/v2#displayId, pICH45195_seq
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://purl.org/dc/terms/title, AtRbcS(at5g38420) 5' UTR
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation3
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation3
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/genBankConversion#label, Rbcs 1B 5'UTR
- http://www.async.ece.utah.edu/pICH45195, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation2
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation3/range
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation7/range
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation4
- http://www.async.ece.utah.edu/pICH45195_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation3/range
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://purl.org/dc/terms/title, AtRbcS (at5g38420) promoter
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation1/range
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation1
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation5/range
- http://www.async.ece.utah.edu/pICH45195, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation0/range
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation5
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation4/range
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45195_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGGCTTAAGTGGGCCGTAAGTGCAATTGCGTTGTGCTCCAAAAGGAACGGTGCCGTGGGTTCCTCTTGTTCATCAGAAATATATTAATTAGCCGTAAAACCTGAAAATTCACAAGCATTTGGATTGTTTTCTAATTTAATATCCATTATGTGACTAAAAGTTCTAGTGATCGTACATACTACATAGAAAATAATAACACAAAATACTAGTTTACATTTCCCAATTAAAAACCATTTTGAATGAACTCTGTCTGATTTAATTATACTTTTAAAATGTGGGATGAATTCAAAGATTATACTTATATTCTTATTATTTAAGATTATCAAGTGGAAAAATAAAAATATGAATGTGTTAATATAAGGTAATAGAAATTTAATCATTTTTTTAATCTATATGTAAAAAGTATTTAACCGATATCTACAATTTGACGCCTCCCAATTGAAAGGAGCCAAAAGCAACCGATCAAGTGCAGACCAGTAGCCATACACATTCACTCCTACCCTTACATGAGAAAGATAAGATTATGGAGTTTTCTGCCACGTGATCTTATCCTAGTGGTCCAAATCGATAAGGGTGTCAACACCTTTCCTTAATCCTGTGGCAATTAACGACGTTATCATGAATTATGGCCCCTTTGATCATTAGGGCTAGTTGCCTCTAGCGGTTCCCACTATATAAAGATGACAAAACCAACAGACAAACAAGTAAGTAAGAGAAAAACCAAAAGAAGAAGAGAAACAACAAGAAGAAGT
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/genBankConversion#label, AtRbcS (at5g38420) promoter
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/genBankConversion#label, AtRbcS2B
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation5
- http://www.async.ece.utah.edu/pICH45195_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195_seq
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation6
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45195_seq
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45195/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation6/range
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45195_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation6/range
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation6
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation4
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45195
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45195, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation7
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45195/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation2/range
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://sbols.org/v2#end, 3001
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation4/range
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45195/annotation7/range, http://sbols.org/v2#start, 2947
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation0
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://sbols.org/v2#end, 2946
- http://www.async.ece.utah.edu/pICH45195/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation7
- http://www.async.ece.utah.edu/pICH45195/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45195/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45195/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45195/annotation5, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45195/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45195/annotation5/range
- http://www.async.ece.utah.edu/pICH45195, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45195/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45195/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation1/range
- http://www.async.ece.utah.edu/pICH45195, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45195/annotation2
- http://www.async.ece.utah.edu/pICH45195/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45195/annotation2/range
- http://www.async.ece.utah.edu/pICH45195/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45195/annotation7, http://sbols.org/genBankConversion#label, AtRbcS(at5g38420) 5' UTR
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45195/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45195, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45195.xml:
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45195.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:41 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:42 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45195.xml
-Python Score = 8
-Java Score = 66
-Number of Files = 92
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45214.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45214.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45214, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45214, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://purl.org/dc/terms/title, LHB1B1 promoter
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation5/range
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45214, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation7
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation1
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation2
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation4
- http://www.async.ece.utah.edu/pICH45214, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45214
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation5/range
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#displayId, pICH45214
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation2/range
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation1/range
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation4
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/genBankConversion#label, LHB1B1 promoter
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation6
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://purl.org/dc/terms/title, LHB1B1 5'UTR
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation7/range
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation0
- http://www.async.ece.utah.edu/pICH45214_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGATATGACTGGTAAGTTTTTCTTGCCAATACGAATTAGAAAACATGTCTTTGAAGATGAACTGTATTTTTTTTTTTTACTTTGTTGTCATTTTAATGTACTTTCTTATCAGGATTAAATCTTCTGTAATTTAGAGTAGTTTTTTTAACAAGATAATTAACAAACTTAGAGTAATGAAAATTGAGATGTTCAGTTTTCACTCATATTTCACATTTTGGTGAAAGAGTGGGTAGTATGCAACGTTCTAAGTATGTTTGGACTTTGTATCATGTTGTTTTGATTCTTTGACGACATGTCTATTTGGGAAACACCAATGACGTGTACCTTGAGACTGATACGATTCAAAGGGATAGAAACACGTCAGATTTACAAGTGGCACCTCTTCAATGGACAATGGGTATTCCAATATGCTAAGATGCTACGAGATATCTAATTTATCTAACACAACTCAATTCCAAACCAAAAATCTGATGCCAGCTCGACAAGACAAAAAATCTAAGCTCAAAAATGTCAACAACCAATAGAAATCAAGGCATTGACGATATCACGAGATAAGCAAATTAAATCTTCAAGTTTTGCAATTCATATGTACGTTATAAATACCCAAAAACCTCACCGTAACCTAGCTATCCAATTTCATCACATCTTATTAACTAAAGAGCCTTTTACTTGCGCCACACTCTCACCGC
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation7/range
- http://www.async.ece.utah.edu/pICH45214_seq, http://sbols.org/v2#displayId, pICH45214_seq
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/genBankConversion#label, LHB1B1 5'UTR
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation6/range
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation0
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation0/range
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation0/range
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation2
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45214_seq
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://sbols.org/v2#start, 2882
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45214/annotation6/range, http://sbols.org/v2#end, 2881
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45214/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation5
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://sbols.org/v2#end, 2938
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation6/range
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation7
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation4/range
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation3
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation4/range
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation1/range
- http://www.async.ece.utah.edu/pICH45214_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45214/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation3/range
- http://www.async.ece.utah.edu/pICH45214/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation5
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45214/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45214/annotation3/range
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45214/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation6
- http://www.async.ece.utah.edu/pICH45214/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45214, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45214/annotation1
- http://www.async.ece.utah.edu/pICH45214/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45214/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45214/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation3
- http://www.async.ece.utah.edu/pICH45214, http://www.ncbi.nlm.nih.gov/genbank#date, 4-DEC-2009
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214/annotation2/range
- http://www.async.ece.utah.edu/pICH45214/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45214_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45214_seq
- http://www.async.ece.utah.edu/pICH45214/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45214/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45214/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45214/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45214.xml:
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45214.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:44 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:45 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Comparing original SBOL2 to converted SBOL2 using Java
-Validation successful, no errors.
-Java conversion matches for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45214.xml
-Python Score = 8
-Java Score = 67
-Number of Files = 93
-File: /Users/myers/git/SBOLTestSuite/SBOL2/pICH45234.xml
-Using Python to convert SBOL2 to SBOL3
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Using Python to convert SBOL3 to SBOL2
-/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/object.py:71: UserWarning: Using a default namespace. To set a namespace use set_namespace()
- warnings.warn('Using a default namespace.'
-Traceback (most recent call last):
- File "/Users/myers/git/SBOL-utilities/path/to/venv/bin/sbol-converter", line 8, in
- sys.exit(main())
- ~~~~^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 465, in main
- command_line_converter(args_dict)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 434, in command_line_converter
- doc2 = convert3to2(doc3, args_dict['force_new_converter'])
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/conversion.py", line 184, in convert3to2
- return sbol_utilities.sbol3_sbol2_conversion.convert3to2(doc3)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 810, in convert3to2
- converter = SBOL3To2ConversionVisitor(doc3)
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 38, in __init__
- self._convert(doc3)
- ~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 55, in _convert
- doc3.accept(self)
- ~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/document.py", line 610, in accept
- return visitor.visit_document(self)
- ~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 269, in visit_document
- obj.accept(self)
- ~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol3/component.py", line 67, in accept
- return visitor.visit_component(self)
- ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
- File "/Users/myers/git/SBOL-utilities/path/to/venv/lib/python3.13/site-packages/sbol_utilities/sbol3_sbol2_conversion.py", line 193, in visit_component
- raise NotImplementedError('Conversion of Component features from SBOL3 to SBOL2 not yet implemented')
-NotImplementedError: Conversion of Component features from SBOL3 to SBOL2 not yet implemented
-Comparing original SBOL2 to converted SBOL2 using Python
-Triples in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45234.xml, not in python32.xml:
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/genBankConversion#label, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://sbols.org/v2#start, 1401
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234, http://www.ncbi.nlm.nih.gov/genbank#division, UNA
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://sbols.org/v2#start, 2248
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation6/range
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://purl.org/dc/terms/title, G to A
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation2
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/genBankConversion#featureType, Promoter
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation4/range
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000316
- http://www.async.ece.utah.edu/pICH45234_seq, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://sbols.org/v2#start, 3051
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/genBankConversion#featureType, Mutation
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/genBankConversion#label, AtRbcS2B
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/genBankConversion#vntifkey, 21
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://sbols.org/v2#orientation, http://sbols.org/v2#reverseComplement
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation0
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://sbols.org/v2#end, 3050
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation5
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://purl.org/dc/terms/title, ORI
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation5
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/v2#displayId, annotation0
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://sbols.org/v2#end, 2015
- http://www.async.ece.utah.edu/pICH45234_seq, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://purl.org/dc/terms/title, AtRbcs2B 5'UTR
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation7/range
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation4
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation6/range
- http://www.async.ece.utah.edu/pICH45234, http://www.ncbi.nlm.nih.gov/genbank#date, 3-JUN-2009
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation3/range
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000804
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation3/range
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://sbols.org/v2#start, 1208
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/v2#displayId, annotation2
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/genBankConversion#featureType, Misc._Feature
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/genBankConversion#vntifkey, 52
- http://www.async.ece.utah.edu/pICH45234_seq, http://sbols.org/v2#displayId, pICH45234_seq
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://purl.org/dc/terms/title, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://sbols.org/v2#end, 4
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://sbols.org/v2#start, 2000
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation0
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://sbols.org/v2#end, 2251
- http://www.async.ece.utah.edu/pICH45234, http://www.ncbi.nlm.nih.gov/genbank#comment, This file is created by Vector NTI http://www.invitrogen.com/
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/genBankConversion#note, RNaseH cleavage point
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://purl.org/dc/terms/title, AtRbcS2B promoter
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation2/range
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://sbols.org/v2#start, 1
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#displayId, pICH45234
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/genBankConversion#label, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/genBankConversion#label, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation1/range
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/v2#displayId, annotation1
- http://www.async.ece.utah.edu/pICH45234/annotation3/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation1
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/v2#displayId, annotation3
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234, http://www.ncbi.nlm.nih.gov/genbank#molecule, DNA
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation7
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation0/range
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation1/range
- http://www.async.ece.utah.edu/pICH45234_seq, http://sbols.org/v2#elements, AATGTGAGACCACGAAGTGGCTCTTCAGTGGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCATTACGTAAAAGGCGAGATCACCAAGGTAGTCGGCAAATAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATCACTCTGTGGTCTCAGGAGCGGGCTTGATTCGATATTAATATGGGATGGTGTACAACGGGTGAAATTTTAGAATTGACTGGTTTGAGTTGATAATAATTTGCGATAGAACTAGGAGTGAAATCCTAGAATGACAATCAAGTTATTATTATACAATTAAATACTACCACAGGTGAAATCCTAGAATTGACGGGTTTGATTCGATATTAATATGGGATGGTGTACTACGGGTGAAATCCGAGAAACAACAATCAAAATACAATTATACAATATTAAACATTTAACAAAATAAACAAATACAACTTAAAACTTTAAAATTTGAGTTATAAAATTTTGTCTCGCGGTGAATTATACATTTAAATCAAACAATAGCAGAAATTTATTAAGTCATCCTAAGAAATATTCAATTATTTTTTATTTAATGAAAATATAGACCCGCGGTATACCGCGGATTAATATTTAGTGCTATTGATAAATTTATCTCAACGTTCAGCTTTGACATTGTGAAATGCATTATGAGTCATGACTCTGTTTATAGATATTCCTGTTATAGTATTTATTAACCGAAGTAATGTAAACCAAATTTTAAAAATACATACAAGATAAATAAAAGGTCCAAAACATTATATTTACGGTCATGCATCTGATTTCTTTTCTTCCAAAAGGAAGGAGCCAAAGCAACCGATCAAGTGGAGACTAGTAAACCATACACAATCACTCATTTCCTCACAAAAGAAAGATAAGATAAGGGTGTCAACACCTTTCCTTAATCATGTGGTAGTGAACGAGTTATCATGAATCCCGGACCCTTTGATCATTAGGGCTTTTTGCCTCTTACGGTTCTCACTATATAAAGATGACAAAACCAATAGAAAAACAATTAAGCAAAAGAAGAAGAAGAAGAAGT
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/genBankConversion#label, G to A
- http://www.async.ece.utah.edu/pICH45234, http://www.ncbi.nlm.nih.gov/genbank#locus, pICH45234
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation7
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/v2#displayId, annotation6
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://purl.org/dc/terms/title, rep (pMB1)
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#type, http://identifiers.org/so/SO:0000988
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation0/range
- http://www.async.ece.utah.edu/pICH45234, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#ComponentDefinition
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation4
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/genBankConversion#label, ORI
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://sbols.org/v2#end, 3137
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/genBankConversion#featureType, Misc._feature
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation3
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation3
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation4/range
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://sbols.org/v2#end, 1241
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://purl.org/dc/terms/title, Sm/Sp no DraIII
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/genBankConversion#vntifkey, 29
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/v2#displayId, annotation7
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/v2#displayId, annotation5
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/genBankConversion#featureType, 5'_UTR
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation7/range
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation5/range
- http://www.async.ece.utah.edu/pICH45234_seq, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234_seq
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation2/range, http://sbols.org/v2#end, 1208
- http://www.async.ece.utah.edu/pICH45234/annotation7/range, http://sbols.org/v2#displayId, range
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation6
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/genBankConversion#featureType, Replication_ori
- http://www.async.ece.utah.edu/pICH45234/annotation0, http://sbols.org/genBankConversion#label, AATG 4bp overhang
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/v2#displayId, annotation4
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation1
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation5/range
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequenceAnnotation, http://www.async.ece.utah.edu/pICH45234/annotation6
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://sbols.org/v2#start, 2252
- http://www.async.ece.utah.edu/pICH45234/annotation6, http://sbols.org/genBankConversion#label, AtRbcS2B promoter
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#sequence, http://www.async.ece.utah.edu/pICH45234_seq
- http://www.async.ece.utah.edu/pICH45234/annotation0/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation4/range, http://sbols.org/v2#end, 2000
- http://www.async.ece.utah.edu/pICH45234/annotation4, http://sbols.org/genBankConversion#vntifkey, 33
- http://www.async.ece.utah.edu/pICH45234/annotation1, http://sbols.org/genBankConversion#vntifkey, 4
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://sbols.org/v2#start, 231
- http://www.async.ece.utah.edu/pICH45234, http://sbols.org/v2#type, http://www.biopax.org/release/biopax-level3.owl#DnaRegion
- http://www.async.ece.utah.edu/pICH45234/annotation6/range, http://sbols.org/v2#orientation, http://sbols.org/v2#inline
- http://www.async.ece.utah.edu/pICH45234/annotation7, http://sbols.org/genBankConversion#label, AtRbcs2B 5'UTR
- http://www.async.ece.utah.edu/pICH45234/annotation5/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pICH45234/annotation2
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/v2#location, http://www.async.ece.utah.edu/pICH45234/annotation2/range
- http://www.async.ece.utah.edu/pICH45234/annotation1/range, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Range
- http://www.async.ece.utah.edu/pICH45234/annotation2, http://sbols.org/genBankConversion#vntifkey, 62
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://purl.org/dc/terms/title, GGAG 4bp overhang
- http://www.async.ece.utah.edu/pICH45234/annotation5, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#SequenceAnnotation
- http://www.async.ece.utah.edu/pICH45234/annotation3, http://sbols.org/v2#role, http://identifiers.org/so/SO:0000110
-Triples in python32.xml, not in /Users/myers/git/SBOLTestSuite/SBOL2/pICH45234.xml:
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#displayId, pLactetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#displayId, tetRSeq
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/tetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#displayId, pLacSeq
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#persistentIdentity, http://www.async.ece.utah.edu/pLactetRSeq
- http://www.async.ece.utah.edu/pLacSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#elements, ACGTURYSWKMBDHVN-.
- http://www.async.ece.utah.edu/tetRSeq/1.0, http://www.w3.org/1999/02/22-rdf-syntax-ns#type, http://sbols.org/v2#Sequence
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#version, 1.0
- http://www.async.ece.utah.edu/pLactetRSeq/1.0, http://sbols.org/v2#encoding, http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
-Python conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pICH45234.xml
-Using Java to convert SBOL2 to SBOL3
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:47 PM org.hibernate.validator.internal.util.Version
-INFO: HV000001: Hibernate Validator null
-Using Java to convert SBOL3 to SBOL2
-SLF4J(W): No SLF4J providers were found.
-SLF4J(W): Defaulting to no-operation (NOP) logger implementation
-SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
-Oct 21, 2025 12:21:48 PM org.hibernate.validator.internal.util.Version