Mercurial > repos > tduigou > sbml2sbol
changeset 0:f0a06f526c7f draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Thu, 09 Dec 2021 14:21:48 +0000 |
| parents | |
| children | 83108f3c65aa |
| files | sbml2sbol.xml test-data/lycopene.xml test-data/sbol_lycopene_output.xml |
| diffstat | 3 files changed, 2226 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sbml2sbol.xml Thu Dec 09 14:21:48 2021 +0000 @@ -0,0 +1,83 @@ +<tool id="sbml2sbol" name="SbmlToSbol" version="0.1.12"> + <description>Convert sbml to sbol format</description> + <requirements> + <requirement type="package" version="0.1.12">sbml2sbol</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m sbml2sbol + --input '$sbml_single_input' + --outfile '$sbol_outfile' + #if str($adv.rbs) == "true" + --rbs True + #else + --rbs False + #end if + --max_prot_per_react '$adv.max_prot_per_react' + #if $adv.tirs + --tirs $adv.tirs + #end if + --pathway_id '$adv.pathway_id' + --uniprotID_key '$adv.uniprotID_key' + ]]></command> + <inputs> + <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" /> + <param name="max_prot_per_react" type="integer" value="3" label="The maximum number of proteins per reaction" /> + <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" /> + <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" /> + <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" /> + </section> + </inputs> + <outputs> + <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="sbml_single_input" value="lycopene.xml" /> + <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/> + </test> + </tests> + <help><![CDATA[ +SBML to SBOL +================ + +Convert a single or multiple SBML files to SBOL. + +Input +----- + +Required: + +* **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s). + +Advanced options: + +* **rbs**\ : (boolean) Calculate or not the RBS strength (default: True). +* **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3). +* **tirs**\ : (int) The RBS strength values (default: None) +* **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway) +* **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy) + +Output +------ + +* **outfile**\ : (string) specify output (SBOL) file. + +Project Links +------------------ + +* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_ + +Version +---------- +0.1.12 + +License +------- + +* `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_ + + ]]></help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lycopene.xml Thu Dec 09 14:21:48 2021 +0000 @@ -0,0 +1,625 @@ +<?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="f9b1ff022aa2133fc1e5e5d1fbac90ac29a744e960a2774be646bc71471ed597" id="RP_model_002_0001" name="002_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 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value="TRS_0_2_740"/> + <brsynth:rule_ids> + <brsynth:RR-02-0c33a3bfd9bf5ad5-14-F/> + <brsynth:RR-02-6692e4af37fbca2d-14-F/> + </brsynth:rule_ids> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR132231/> + <brsynth:MNXR112683/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5706379442030705"/> + <brsynth:idx_in_path value="1"/> + <brsynth:selenzy_P21684> + <brsynth:score value="91.109"/> + <brsynth:target_ID value="553"/> + </brsynth:selenzy_P21684> + <brsynth:selenzy_P21683> + <brsynth:score value="47.678"/> + <brsynth:target_ID value="553"/> + </brsynth:selenzy_P21683> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-1544.3333670420595"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-1561.4482045767807"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-1544.3333670420595"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-1881.1378556154446"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM100" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM83" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM11" stoichiometry="2" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0"> + <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="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/uniprot/P21684"/> + <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.32"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth 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<brsynth:MNXR113543/> + <brsynth:MNXR118024/> + <brsynth:MNXR139549/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5518755963407151"/> + <brsynth:idx_in_path value="2"/> + <brsynth:selenzy_P21683> + <brsynth:score value="91.9"/> + <brsynth:target_ID value="553"/> + </brsynth:selenzy_P21683> + <brsynth:selenzy_P21684> + <brsynth:score value="74.885"/> + <brsynth:target_ID value="553"/> + </brsynth:selenzy_P21684> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-119.13360567395966"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-153.36328074340173"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-119.13360567395966"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-1501.0650763644926"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM11" stoichiometry="2" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" 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<groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000001"/> + <groups:member groups:idRef="MNXM100"/> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="CMPD_0000000003"/> + <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="MNXM100"/> + <groups:member groups:idRef="MNXM11"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_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="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM24"/> + <groups:member groups:idRef="MNXM8975"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_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="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM24"/> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM8975"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sbol_lycopene_output.xml Thu Dec 09 14:21:48 2021 +0000 @@ -0,0 +1,1518 @@ +<?xml version="1.0" ?> +<rdf:RDF xmlns:sys-bio="http://sys-bio.org#" xmlns:sbol="http://sbols.org/v2#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#"> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_30000_rbs/1"> + <sbol:displayId>P21687_30000_rbs</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_30000_rbs"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/1"> + <sbol:displayId>P21687_10000_gene</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:version>1</sbol:version> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_5_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/> + <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_5_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_rbs_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_rbs/1"/> + <sbol:displayId>P21687_10000_rbs_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_rbs_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_cds_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_cds/1"/> + <sbol:displayId>P21687_10000_cds_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_cds_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_3_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/> + <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_3_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_0/1"> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_rbs_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_0"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_5_prime_assembly_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_1/1"> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_cds_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_rbs_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_2/1"> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/rxn_3_3_prime_assembly_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/constraint_2"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_gene/P21687_10000_cds_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_cds/1"> + <sbol:displayId>P21687_10000_cds</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_cds"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_rbs/1"> + <sbol:displayId>P21687_10000_rbs</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21687_10000_rbs"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:version>1</sbol:version> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/1"> + <sbol:displayId>P21685_30000_gene</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:version>1</sbol:version> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_5_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/> + <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_5_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_rbs_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_rbs/1"/> + <sbol:displayId>P21685_30000_rbs_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_rbs_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_cds_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_cds/1"/> + <sbol:displayId>P21685_30000_cds_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_cds_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_3_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/> + <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_3_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_0/1"> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_rbs_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_0"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_5_prime_assembly_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_1/1"> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_cds_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_rbs_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_2/1"> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/rxn_3_3_prime_assembly_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/constraint_2"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_30000_gene/P21685_30000_cds_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/1"> + <sbol:displayId>P21685_20000_gene</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:version>1</sbol:version> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/rxn_3_5_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/> + <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/rxn_3_5_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_rbs_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_rbs/1"/> + <sbol:displayId>P21685_20000_rbs_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_rbs_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_cds_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_cds/1"/> + <sbol:displayId>P21685_20000_cds_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_cds_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/rxn_3_3_prime_assembly_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/> + <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/rxn_3_3_prime_assembly_0"/> + <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/constraint_0/1"> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_rbs_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/constraint_0"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/rxn_3_5_prime_assembly_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/constraint_1/1"> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_cds_0/1"/> + <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/constraint_1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21685_20000_gene/P21685_20000_rbs_0/1"/> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint 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