Mercurial > repos > tduigou > rpbasicdesign
changeset 1:de9f53630349 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Wed, 15 Dec 2021 15:10:43 +0000 |
| parents | e8e8050e9997 |
| children | 8a087d7546b8 |
| files | rpbasicdesign.xml rpbasicdesign/rpbasicdesign.xml rpbasicdesign/test-data/BASIC_construct_A1.xml rpbasicdesign/test-data/BASIC_construct_B1.xml rpbasicdesign/test-data/BASIC_construct_C1.xml rpbasicdesign/test-data/biolegio_plate.csv rpbasicdesign/test-data/constructs.csv rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml rpbasicdesign/test-data/user_parts_plate.csv test-data/BASIC_construct_A1.xml test-data/BASIC_construct_B1.xml test-data/BASIC_construct_C1.xml test-data/biolegio_plate.csv test-data/constructs.csv test-data/lycopene_CrtEBI_from_selenzy.xml test-data/user_parts_plate.csv |
| diffstat | 16 files changed, 1625 insertions(+), 1625 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign.xml Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,121 @@ +<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> + <description>Build DNA-BOT input files from rpSBML</description> + <requirements> + <requirement type="package" version="0.3.4">rpbasicdesign</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rpbasicdesign.cli + --rpsbml_file '$rpsbml_file' + #if $adv.parts_files + #set files = '" "'.join([str($file) for $file in $adv.parts_files]) + --parts_files "${files}" + #end if + --lms_id '$adv.lms_id' + --lmp_id '$adv.lmp_id' + --backbone_id '$backbone_id' + --sample_size '$sample_size' + #if str($adv.cds_permutation) == "true" + --cds_permutation true + #else + --cds_permutation false + #end if + --o_dnabot_dir 'out/dnabot_in' + --o_sbol_dir 'out/sbol_export' + ]]></command> + <inputs> + <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/> + <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> + <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" /> + <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> + <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> + <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> + </section> + </inputs> + <outputs> + <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" /> + <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/> + <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/> + <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs"> + <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> + </collection> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced --> + <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> + <param name="sample_size" value="3" /> + <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/> + <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/> + <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/> + <output_collection name="sbol_dir" type="list"> + <element name="BASIC_construct_A1" ftype="xml" value="BASIC_construct_A1.xml" sort="true"/> + <element name="BASIC_construct_B1" ftype="xml" value="BASIC_construct_B1.xml" sort="true"/> + <element name="BASIC_construct_C1" ftype="xml" value="BASIC_construct_C1.xml" sort="true"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ +rpbasicdesign +================ + +Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding +enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly +chosen from a default list. CDSs, in other words gene variants, of enzymes are +randomly chosen from amongst the UniProt IDs extracted. Constructs generated +can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL +files. + +Input +----- + +Required: + +* **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. + +Advanced options: + +* **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv] +* **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. +* **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. +* **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. +* **sample_size**\ : (int) Number of construct to generate.Default: 3. +* **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. + +Output +------ + +* **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in. +* **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rpbasicdesign>`_ + +License +------- + +* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ + + ]]></help> + <citations> + <citation type="bibtex"> + @article{10.1093/synbio/ysaa010, + author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, + title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, + journal = {Synthetic Biology}, + volume = {5}, + number = {1}, + year = {2020}, + month = {07}, + issn = {2397-7000}, + doi = {10.1093/synbio/ysaa010}, + url = {https://doi.org/10.1093/synbio/ysaa010}, + note = {ysaa010}, + eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, + } + </citation> + </citations> +</tool> \ No newline at end of file
--- a/rpbasicdesign/rpbasicdesign.xml Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> - <description>Build DNA-BOT input files from rpSBML</description> - <requirements> - <requirement type="package" version="0.3.4">rpbasicdesign</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - python -m rpbasicdesign.cli - --rpsbml_file '$rpsbml_file' - #if $adv.parts_files - #set files = '" "'.join([str($file) for $file in $adv.parts_files]) - --parts_files "${files}" - #end if - --lms_id '$adv.lms_id' - --lmp_id '$adv.lmp_id' - --backbone_id '$backbone_id' - --sample_size '$sample_size' - #if str($adv.cds_permutation) == "true" - --cds_permutation true - #else - --cds_permutation false - #end if - --o_dnabot_dir 'out/dnabot_in' - --o_sbol_dir 'out/sbol_export' - ]]></command> - <inputs> - <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/> - <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> - <param name="sample_size" type="integer" value="3" label="Number of construct to generate" /> - <section name="adv" title="Advanced Options" expanded="false"> - <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" /> - <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> - <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> - <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> - </section> - </inputs> - <outputs> - <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" /> - <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/> - <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/> - <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs"> - <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> - </collection> - </outputs> - <tests> - <test> - <!-- test 1: check if identical outputs are produced --> - <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> - <param name="sample_size" value="3" /> - <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/> - <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/> - <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/> - <output_collection name="sbol_dir" type="list"> - <discovered_dataset designation="BASIC_construct_A1" ftype="xml" file="BASIC_construct_A1.xml"/> - <discovered_dataset designation="BASIC_construct_B1" ftype="xml" file="BASIC_construct_B1.xml"/> - <discovered_dataset designation="BASIC_construct_C1" ftype="xml" file="BASIC_construct_C1.xml"/> - </output_collection> - </test> - </tests> - <help><![CDATA[ -rpbasicdesign -================ - -Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding -enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly -chosen from a default list. CDSs, in other words gene variants, of enzymes are -randomly chosen from amongst the UniProt IDs extracted. Constructs generated -can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL -files. - -Input ------ - -Required: - -* **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. - -Advanced options: - -* **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv] -* **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. -* **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. -* **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. -* **sample_size**\ : (int) Number of construct to generate.Default: 3. -* **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. - -Output ------- - -* **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in. -* **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export. - -Project Links ------------------- - -* `GitHub <https://github.com/brsynth/rpbasicdesign>`_ - -License -------- - -* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ - - ]]></help> - <citations> - <citation type="bibtex"> - @article{10.1093/synbio/ysaa010, - author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, - title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, - journal = {Synthetic Biology}, - volume = {5}, - number = {1}, - year = {2020}, - month = {07}, - issn = {2397-7000}, - doi = {10.1093/synbio/ysaa010}, - url = {https://doi.org/10.1093/synbio/ysaa010}, - note = {ysaa010}, - eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, - } - </citation> - </citations> -</tool> \ No newline at end of file
--- a/rpbasicdesign/test-data/BASIC_construct_A1.xml Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMS</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMP</sbol:displayId> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1"> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:displayId>PJ23119_BASIC</sbol:displayId> - <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1"> - <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:displayId>U1_RBS1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1"> - <sbol:displayId>U2_RBS1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/> - <sbol:version>1</sbol:version> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> - <sbol:displayId>P21683</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> - <sbol:version>1</sbol:version> - <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> - <sbol:displayId>P21685</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/1"> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"> - <sbol:displayId>U3_RBS2_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5/1"> - <sbol:version>1</sbol:version> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> - <sbol:displayId>constraint_5</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7/1"> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> - <sbol:displayId>constraint_7</sbol:displayId> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:version>1</sbol:version> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"> - <sbol:version>1</sbol:version> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>U1_RBS1_0</sbol:displayId> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0"/> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21684_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> - <sbol:displayId>LMS_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0"/> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> - <sbol:displayId>P21683_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0"/> - </sbol:Component> - </sbol:component> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1"/> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>constraint_8</sbol:displayId> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2/1"> - <sbol:displayId>constraint_2</sbol:displayId> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> - <sbol:displayId>BASIC_construct_A1</sbol:displayId> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0/1"> - <sbol:displayId>constraint_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6/1"> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_6</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC/1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>PJ23119_BASIC_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0"/> - <sbol:version>1</sbol:version> - <sbol:displayId>U2_RBS1_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3/1"> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> - <sbol:version>1</sbol:version> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3"/> - <sbol:displayId>constraint_3</sbol:displayId> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21685_0</sbol:displayId> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1/1"> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> - <sbol:displayId>constraint_1</sbol:displayId> - <sbol:version>1</sbol:version> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> - <sbol:displayId>constraint_4</sbol:displayId> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - </sbol:ComponentDefinition> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> - <sbol:displayId>LMS</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements></sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/> - <sbol:elements></sbol:elements> - <sbol:displayId>PJ23119_BASIC</sbol:displayId> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1"> - <sbol:elements></sbol:elements> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:displayId>U1_RBS1</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1"> - <sbol:displayId>U2_RBS1</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements></sbol:elements> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:displayId>P21683</sbol:displayId> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:displayId>P21685</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - </sbol:Sequence> -</rdf:RDF>
--- a/rpbasicdesign/test-data/BASIC_construct_B1.xml Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMS</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMP</sbol:displayId> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:displayId>PJ23101_BASIC</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1"> - <sbol:displayId>U1_RBS3</sbol:displayId> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:version>1</sbol:version> - <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1"> - <sbol:displayId>U2_RBS1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/> - <sbol:version>1</sbol:version> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> - <sbol:displayId>P21683</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> - <sbol:version>1</sbol:version> - <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> - <sbol:displayId>P21685</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/1"> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1/1"> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - <sbol:displayId>constraint_1</sbol:displayId> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21684_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> - </sbol:Component> - </sbol:component> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7"/> - <sbol:version>1</sbol:version> - <sbol:displayId>constraint_7</sbol:displayId> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>U2_RBS1_0</sbol:displayId> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3/1"> - <sbol:displayId>constraint_3</sbol:displayId> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6/1"> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_6</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6"/> - <sbol:version>1</sbol:version> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"> - <sbol:displayId>U3_RBS2_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4/1"> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_4</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4"/> - <sbol:version>1</sbol:version> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS3/1"/> - <sbol:displayId>U1_RBS3_0</sbol:displayId> - </sbol:Component> - </sbol:component> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1"/> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5/1"> - <sbol:displayId>constraint_5</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1"> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:version>1</sbol:version> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> - <sbol:displayId>LMS_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0"/> - </sbol:Component> - </sbol:component> - <sbol:displayId>BASIC_construct_B1</sbol:displayId> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1"> - <sbol:displayId>P21685_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0"/> - <sbol:version>1</sbol:version> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"> - <sbol:version>1</sbol:version> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0"/> - <sbol:displayId>PJ23101_BASIC_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8/1"> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - <sbol:displayId>constraint_8</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21683_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> - <sbol:version>1</sbol:version> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - <sbol:displayId>constraint_0</sbol:displayId> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:version>1</sbol:version> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2/1"> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_2</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - </sbol:ComponentDefinition> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> - <sbol:displayId>LMS</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements></sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/> - <sbol:displayId>PJ23101_BASIC</sbol:displayId> - <sbol:elements></sbol:elements> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/> - <sbol:elements></sbol:elements> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:displayId>U1_RBS3</sbol:displayId> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1"> - <sbol:displayId>U2_RBS1</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements></sbol:elements> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:displayId>P21683</sbol:displayId> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:displayId>P21685</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - </sbol:Sequence> -</rdf:RDF>
--- a/rpbasicdesign/test-data/BASIC_construct_C1.xml Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ -<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMS</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> - <sbol:displayId>LMP</sbol:displayId> - <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:displayId>PJ23101_BASIC</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1"> - <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:displayId>U1_RBS1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> - <sbol:version>1</sbol:version> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> - <sbol:version>1</sbol:version> - <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> - <sbol:displayId>P21685</sbol:displayId> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS2/1"> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> - <sbol:displayId>U2_RBS2</sbol:displayId> - <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS2/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS2"/> - <sbol:version>1</sbol:version> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> - <sbol:displayId>P21683</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> - <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> - </sbol:ComponentDefinition> - <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1"/> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21685_0</sbol:displayId> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0"/> - <sbol:version>1</sbol:version> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:displayId>P21684_0</sbol:displayId> - </sbol:Component> - </sbol:component> - <sbol:version>1</sbol:version> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6/1"> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_6</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4/1"> - <sbol:displayId>constraint_4</sbol:displayId> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0"/> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP_0</sbol:displayId> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> - </sbol:Component> - </sbol:component> - <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1"> - <sbol:displayId>P21683_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0"/> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> - </sbol:Component> - </sbol:component> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS2/1"/> - <sbol:displayId>U2_RBS2_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5/1"> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/> - <sbol:version>1</sbol:version> - <sbol:displayId>constraint_5</sbol:displayId> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8/1"> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_8</sbol:displayId> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1"/> - <sbol:version>1</sbol:version> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2/1"> - <sbol:displayId>constraint_2</sbol:displayId> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2"/> - <sbol:version>1</sbol:version> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3/1"> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/> - <sbol:displayId>constraint_3</sbol:displayId> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1"> - <sbol:displayId>LMS_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0"/> - </sbol:Component> - </sbol:component> - <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"> - <sbol:displayId>U1_RBS1_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1/1"> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/> - <sbol:displayId>constraint_1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"> - <sbol:displayId>U3_RBS2_0</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0"/> - </sbol:Component> - </sbol:component> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7"/> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/> - <sbol:displayId>constraint_7</sbol:displayId> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:version>1</sbol:version> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:displayId>BASIC_construct_C1</sbol:displayId> - <sbol:sequenceConstraint> - <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0/1"> - <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1"/> - <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> - <sbol:displayId>constraint_0</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0"/> - <sbol:version>1</sbol:version> - <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> - </sbol:SequenceConstraint> - </sbol:sequenceConstraint> - <sbol:component> - <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"> - <sbol:access rdf:resource="http://sbols.org/v2#public"/> - <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/> - <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0"/> - <sbol:displayId>PJ23101_BASIC_0</sbol:displayId> - <sbol:version>1</sbol:version> - </sbol:Component> - </sbol:component> - </sbol:ComponentDefinition> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> - <sbol:displayId>LMS</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> - <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements></sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:displayId>LMP</sbol:displayId> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/> - <sbol:displayId>PJ23101_BASIC</sbol:displayId> - <sbol:elements></sbol:elements> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1"> - <sbol:elements></sbol:elements> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:displayId>U1_RBS1</sbol:displayId> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> - <sbol:displayId>P21684</sbol:displayId> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> - <sbol:displayId>U3_RBS2</sbol:displayId> - <sbol:elements></sbol:elements> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - <sbol:displayId>P21685</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1"> - <sbol:displayId>U2_RBS2</sbol:displayId> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:version>1</sbol:version> - <sbol:elements></sbol:elements> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/> - </sbol:Sequence> - <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> - <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> - <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> - <sbol:displayId>P21683</sbol:displayId> - <sbol:elements>atgc</sbol:elements> - <sbol:version>1</sbol:version> - </sbol:Sequence> -</rdf:RDF>
--- a/rpbasicdesign/test-data/biolegio_plate.csv Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -L1-S,A1, -L1-P,B1, -L2-S,A2, -L2-P,B2, -L3-S,A3, -L3-P,B3, -L4-S,A4, -L4-P,B4, -L5-S,A5, -L5-P,B5, -L6-S,A6, -L6-P,B6, -LMP-S,A7, -LMP-P,B7, -LMS-S,A8, -LMS-P,B8, -U1-S,C1, -U2-S,C2, -U3-S,C3, -U1-RBS1-P,C4, -U1-RBS2-P,C5, -U1-RBS3-P,C6, -U1-A01-P,D1, -U1-A02-P,D2, -U1-A03-P,D3, -U1-A04-P,D4, -U1-A05-P,D5, -U1-A06-P,D6, -U1-A07-P,D7, -U1-A08-P,D8, -U1-A09-P,D9, -U1-A10-P,D10, -U1-A11-P,D11 -U1-A12-P,D12, -U2-RBS1-P,C7, -U2-RBS2-P,C8, -U2-RBS3-P,C9, -U2-A01-P,E1, -U2-A02-P,E2, -U2-A03-P,E3, -U2-A04-P,E4, -U2-A05-P,E5, -U2-A06-P,E6, -U2-A07-P,E7, -U2-A08-P,E8, -U2-A09-P,E9, -U2-A10-P,E10, -U2-A11-P,E11 -U2-A12-P,E12, -U3-RBS1-P,C10, -U3-RBS2-P,C11, -U3-RBS3-P,C12, -U3-A01-P,F1, -U3-A02-P,F2, -U3-A03-P,F3, -U3-A04-P,F4, -U3-A05-P,F5, -U3-A06-P,F6, -U3-A07-P,F7, -U3-A08-P,F8, -U3-A09-P,F9, -U3-A10-P,F10, -U3-A11-P,F11 -U3-A12-P,F12, -U1-AM12-P,A10, -U1-AM24-P,B10, -U2-AM12-P,A11, -U2-AM24-P,B11, -U3-AM12-P,A12, -U3-AM24-P,B12, -LF1-S,A9, -LF1-P,B9, -LF2-S,G1, -LF2-P,H1, -LF3-S,G2, -LF3-P,H2, -LF4-S,G3, -LF4-P,H3, -LF5-S,G4, -LF5-P,H4, -LF6-S,G5, -LF6-P,H5, \ No newline at end of file
--- a/rpbasicdesign/test-data/constructs.csv Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 -A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
--- a/rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,393 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> - <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> - <listOfCompartments> - <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6"> - <bqbiol:is> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/> - <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> - <rdf:li rdf:resource="http://identifiers.org/seed/c"/> - <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> - <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> - <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </annotation> - </compartment> - </listOfCompartments> - <listOfSpecies> - <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46"> - <bqbiol:is> - <rdf:Bag/> - </bqbiol:is> - </rdf:Description> - <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/> - <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/> - <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/> - </brsynth:brsynth> - </rdf:BRSynth> - 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<brsynth:rp2_transfo_id value="TRS_0_0_1"/> - <brsynth:rule_ids> - <brsynth:RR-02-bdf7d8715e2e4d93-16-F/> - </brsynth:rule_ids> - <brsynth:tmpl_rxn_ids> - <brsynth:MNXR113128/> - </brsynth:tmpl_rxn_ids> - <brsynth:rule_score value="0.7486085128675456"/> - <brsynth:idx_in_path value="3"/> - <brsynth:selenzy_P21685> - <brsynth:score value="81.82"/> - <brsynth:target_ID value="553"/> - </brsynth:selenzy_P21685> - <brsynth:selenzy_P21683> - <brsynth:score value="63.183"/> - <brsynth:target_ID value="553"/> - </brsynth:selenzy_P21683> - </brsynth:brsynth> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <listOfReactants> - <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/> - <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="MNXM24" stoichiometry="4" constant="true"/> - <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - </listOfReactions> - <groups:listOfGroups> - <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> - <brsynth:global_score value="-1"/> - </brsynth:brsynth> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <groups:listOfMembers> - <groups:member groups:idRef="rxn_1"/> - <groups:member groups:idRef="rxn_2"/> - <groups:member groups:idRef="rxn_3"/> - </groups:listOfMembers> - </groups:group> - <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <groups:listOfMembers> - <groups:member groups:idRef="CMPD_0000000003"/> - <groups:member groups:idRef="CMPD_0000000001"/> - </groups:listOfMembers> - </groups:group> - <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <groups:listOfMembers> - <groups:member groups:idRef="CMPD_0000000001"/> - <groups:member groups:idRef="MNXM132"/> - <groups:member groups:idRef="CMPD_0000000003"/> - <groups:member groups:idRef="TARGET_0000000001"/> - <groups:member groups:idRef="MNXM83"/> - </groups:listOfMembers> - </groups:group> - <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <groups:listOfMembers> - <groups:member groups:idRef="MNXM8975"/> - <groups:member groups:idRef="MNXM24"/> - <groups:member groups:idRef="MNXM11"/> - </groups:listOfMembers> - </groups:group> - <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> - <annotation> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> - <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> - </rdf:BRSynth> - </rdf:RDF> - </annotation> - <groups:listOfMembers> - <groups:member groups:idRef="MNXM83"/> - <groups:member groups:idRef="MNXM132"/> - <groups:member groups:idRef="MNXM11"/> - </groups:listOfMembers> - </groups:group> - </groups:listOfGroups> - </model> -</sbml>
--- a/rpbasicdesign/test-data/user_parts_plate.csv Thu Nov 18 13:17:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -BASIC_SEVA_37_CmR-p15A.1,A1, -P21683,B1, -P21684,C1, -P21685,D1, -PJ23101_BASIC,E1, -PJ23119_BASIC,F1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BASIC_construct_A1.xml Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,339 @@ +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMS</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMP</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1"> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:displayId>PJ23119_BASIC</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1"> + <sbol:displayId>U2_RBS1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> + <sbol:displayId>P21683</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> + <sbol:displayId>P21685</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/1"> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"> + <sbol:displayId>U3_RBS2_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5/1"> + <sbol:version>1</sbol:version> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> + <sbol:displayId>constraint_5</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> + <sbol:displayId>constraint_7</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:version>1</sbol:version> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>U1_RBS1_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0"/> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21684_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> + <sbol:displayId>LMS_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> + <sbol:displayId>P21683_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0"/> + </sbol:Component> + </sbol:component> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>constraint_8</sbol:displayId> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2/1"> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:displayId>BASIC_construct_A1</sbol:displayId> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0/1"> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_6</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>PJ23119_BASIC_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0"/> + <sbol:version>1</sbol:version> + <sbol:displayId>U2_RBS1_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3/1"> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> + <sbol:version>1</sbol:version> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3"/> + <sbol:displayId>constraint_3</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21685_0</sbol:displayId> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> + <sbol:displayId>constraint_4</sbol:displayId> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + </sbol:ComponentDefinition> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> + <sbol:displayId>LMS</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/> + <sbol:elements></sbol:elements> + <sbol:displayId>PJ23119_BASIC</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1"> + <sbol:elements></sbol:elements> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1"> + <sbol:displayId>U2_RBS1</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>P21683</sbol:displayId> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:displayId>P21685</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + </sbol:Sequence> +</rdf:RDF>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BASIC_construct_B1.xml Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,339 @@ +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMS</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMP</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:displayId>PJ23101_BASIC</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1"> + <sbol:displayId>U1_RBS3</sbol:displayId> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1"> + <sbol:displayId>U2_RBS1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> + <sbol:displayId>P21683</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> + <sbol:displayId>P21685</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/1"> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21684_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> + </sbol:Component> + </sbol:component> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_7"/> + <sbol:version>1</sbol:version> + <sbol:displayId>constraint_7</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>U2_RBS1_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3/1"> + <sbol:displayId>constraint_3</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_3"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6/1"> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_6</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_6"/> + <sbol:version>1</sbol:version> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"> + <sbol:displayId>U3_RBS2_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_4</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_4"/> + <sbol:version>1</sbol:version> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0/1"> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U1_RBS3_0"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS3/1"/> + <sbol:displayId>U1_RBS3_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5/1"> + <sbol:displayId>constraint_5</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U2_RBS1_0/1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21684_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_5"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> + <sbol:displayId>LMS_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0"/> + </sbol:Component> + </sbol:component> + <sbol:displayId>BASIC_construct_B1</sbol:displayId> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1"> + <sbol:displayId>P21685_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0"/> + <sbol:displayId>PJ23101_BASIC_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/U3_RBS2_0/1"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21685_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + <sbol:displayId>constraint_8</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_8"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21683_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/P21683_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_0"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMS_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:version>1</sbol:version> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2/1"> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/PJ23101_BASIC_0/1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/LMP_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + </sbol:ComponentDefinition> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> + <sbol:displayId>LMS</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/> + <sbol:displayId>PJ23101_BASIC</sbol:displayId> + <sbol:elements></sbol:elements> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/> + <sbol:elements></sbol:elements> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:displayId>U1_RBS3</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1"> + <sbol:displayId>U2_RBS1</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>P21683</sbol:displayId> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:displayId>P21685</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + </sbol:Sequence> +</rdf:RDF>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BASIC_construct_C1.xml Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,339 @@ +<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMS</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:displayId>LMP</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:displayId>PJ23101_BASIC</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> + <sbol:version>1</sbol:version> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> + <sbol:displayId>P21685</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS2/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:displayId>U2_RBS2</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS2/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS2"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> + <sbol:displayId>P21683</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1"/> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21685_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0"/> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>P21684_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:version>1</sbol:version> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_6</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_6"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4/1"> + <sbol:displayId>constraint_4</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_4"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> + </sbol:Component> + </sbol:component> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1"> + <sbol:displayId>P21683_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0"/> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS2/1"/> + <sbol:displayId>U2_RBS2_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5/1"> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_5"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21684_0/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>constraint_5</sbol:displayId> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_8</sbol:displayId> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21683_0/1"/> + <sbol:version>1</sbol:version> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_8"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2/1"> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_2"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3/1"> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_3"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"/> + <sbol:displayId>constraint_3</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1"> + <sbol:displayId>LMS_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0"/> + </sbol:Component> + </sbol:component> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0/1"> + <sbol:displayId>U1_RBS1_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U1_RBS1_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMP_0/1"/> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0/1"> + <sbol:displayId>U3_RBS2_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U3_RBS2_0"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_7"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/U2_RBS2_0/1"/> + <sbol:displayId>constraint_7</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/P21685_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:displayId>BASIC_construct_C1</sbol:displayId> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/LMS_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/constraint_0"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_C1/PJ23101_BASIC_0"/> + <sbol:displayId>PJ23101_BASIC_0</sbol:displayId> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + </sbol:ComponentDefinition> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> + <sbol:displayId>LMS</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/> + <sbol:displayId>PJ23101_BASIC</sbol:displayId> + <sbol:elements></sbol:elements> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1"> + <sbol:elements></sbol:elements> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> + <sbol:displayId>P21684</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:displayId>P21685</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1"> + <sbol:displayId>U2_RBS2</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:elements></sbol:elements> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>P21683</sbol:displayId> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> +</rdf:RDF>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate.csv Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs.csv Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lycopene_CrtEBI_from_selenzy.xml Wed Dec 15 15:10:43 2021 +0000 @@ -0,0 +1,393 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> + <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> + <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </compartment> + </listOfCompartments> + <listOfSpecies> + <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/> + <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/> + <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="MNXM132" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/> + <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)"/> + <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="MNXM11" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/> + <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/> + <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth 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