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changeset 0:1a75fa306c76 draft default tip

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planemo upload commit dd818e990b23b010abe4843aaaa7315606b06bd6
author iuc
date Sat, 15 Oct 2022 21:21:53 +0000
parents
children
files sbml2sbol.xml test-data/lycopene.xml test-data/sbol_lycopene_output.xml test-data/sbol_lycopene_output2.xml
diffstat 4 files changed, 4027 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sbml2sbol.xml	Sat Oct 15 21:21:53 2022 +0000
@@ -0,0 +1,90 @@
+<tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Convert sbml to sbol format</description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">0.1.13</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m sbml2sbol
+        --input '$sbml_single_input'
+        --outfile '$sbol_outfile'
+        $adv.rbs
+        --max_prot_per_react '$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="sbml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param argument="--rbs" type="boolean" truevalue="--rbs True" falsevalue="--rbs False" label="Calculate the RBS strength?" checked="true" help="Calculate or not the RBS (Ribosome Binding Site) strength (default: True)"/>
+            <param argument="--max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
+            <param argument="--tirs" type="text" optional="true" label="Space separated RBS strength values" />
+            <param argument="--pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
+                <validator type="empty_field" message="Pathway ID is required"/>
+            </param>
+            <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
+                <validator type="empty_field" message="Uniprot ID is required"/>
+            </param>
+        </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>
+        <test>
+        <!-- test 2: check if identical outputs are produced without RBS calculation  -->
+            <param name="sbml_single_input" value="lycopene.xml" />
+            <param name="rbs" value="--rbs False" />
+            <param name="max_prot_per_react" value="5" />
+            <output name="sbol_outfile" file="sbol_lycopene_output2.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+SBML to SBOL
+================
+
+This tool takes a pathway model (encoded in SBML) as input and returns a collection of placeholders for the subsequent design of the synthetic DNA that is required to encode the enzymes defined in the pathway model (encoded in SBOL).
+
+Input
+-----
+
+Required:
+
+* **Pathway (SBML)**\ : Pathway file in SBML format.
+
+Advanced options:
+
+* **Calculate the RBS strength?**\ : (boolean) Calculate or not the RBS (Ribosome Binding Site) strength (default: True).
+* **The maximum number of proteins per reaction**\ : (int) The maximum number of proteins per reaction (default: 3).
+* **Space separated RBS strength values**\ : (int) The RBS (Ribosome Binding Site) strength values (default: None)
+* **Group ID of the heterologous pathway**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
+* **Uniprot ID**\ : (string) Uniprot ID of the heterologous pathway (default: selenzy)
+
+Output
+------
+
+* **sbol outfile**\ : output (SBOL) file.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
+
+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	Sat Oct 15 21:21:53 2022 +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 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:fba_biomass_shadow_price>
+                  <brsynth:value value="-0.0"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="-1.0"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="936.7141451846444"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" 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="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
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+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-2256.1898491337233"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </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:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-1966.8036657706114"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="MNXM100" 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="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <bqbiol:is>
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+                <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])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
+                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-1719.970141951422"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
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+          </rdf:RDF>
+        </annotation>
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+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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+          <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="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="-0.0"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="-1.0"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="1245.5794452419402"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" 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="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
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+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
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+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-1495.8281099920857"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
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+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" 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="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
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+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([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/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-1828.3274439664424"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </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 rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-2261.3806478863044"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" 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="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21684"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.82"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <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])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]&gt;&gt;[H]OP(=O)(O[H])OP(=O)(O[H])OC([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].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:rp2_transfo_id 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 rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <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])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]&gt;&gt;[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].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-bedda4e2f5001e0c-14-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR111250/>
+                  <brsynth:MNXR111499/>
+                  <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" 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="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21688"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21687"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P21685"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <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]&gt;&gt;[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-ae41ec5771136ea5-14-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR113128/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.7358363677022237"/>
+                <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:selenzy_P21687>
+                  <brsynth:score value="28.174"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21687>
+                <brsynth:selenzy_P21688>
+                  <brsynth:score value="22.44"/>
+                  <brsynth:target_ID value="553"/>
+                </brsynth:selenzy_P21688>
+                <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="1191.8613577748536"/>
+                  <brsynth:error value="44.93683979991009"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="1191.8613577748536"/>
+                  <brsynth:error value="44.93683979991009"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="1191.8613577748536"/>
+                  <brsynth:error value="44.93683979991009"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="329.6284950676197"/>
+                  <brsynth:error value="44.93683979991009"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+              </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:fba_biomass>
+                  <brsynth:value value="0.8769972144269764"/>
+                  <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="-471.6056149411652"/>
+                  <brsynth:error value="47.74843757946335"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="-522.9501275453283"/>
+                  <brsynth:error value="47.74843757946335"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-471.6056149411652"/>
+                  <brsynth:error value="47.74843757946335"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-3052.5744369123167"/>
+                  <brsynth:error value="47.74843757946335"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+                <brsynth:global_score value="0.9892438888549804"/>
+              </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="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	Sat Oct 15 21:21:53 2022 +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>
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+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/rxn_2_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/P21683_30000_gene/P21683_30000_rbs_1/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_rbs/1"/>
+        <sbol:displayId>P21683_30000_rbs_1</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_1"/>
+        <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/P21683_30000_gene/P21683_30000_cds_1/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_cds/1"/>
+        <sbol:displayId>P21683_30000_cds_1</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_cds_1"/>
+        <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/P21683_30000_gene/rxn_2_3_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_2_3_prime_assembly/1"/>
+        <sbol:displayId>rxn_2_3_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/rxn_2_3_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/P21683_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/P21683_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/P21683_30000_gene/P21683_30000_rbs_2/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_rbs/1"/>
+        <sbol:displayId>P21683_30000_rbs_2</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_2"/>
+        <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/P21683_30000_gene/P21683_30000_cds_2/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_cds/1"/>
+        <sbol:displayId>P21683_30000_cds_2</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_cds_2"/>
+        <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/P21683_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/P21683_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/P21683_30000_gene/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_2/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_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/P21683_30000_gene/constraint_1/1">
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_cds_2/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/constraint_1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_2/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/rxn_3_3_prime_assembly_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/constraint_2"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_cds_2/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+</rdf:RDF>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sbol_lycopene_output2.xml	Sat Oct 15 21:21:53 2022 +0000
@@ -0,0 +1,1794 @@
+<?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/P21688_30000_rbs/1">
+    <sbol:displayId>P21688_30000_rbs</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_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/P21688_20000_gene/1">
+    <sbol:displayId>P21688_20000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_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/P21688_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/P21688_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/P21688_20000_gene/P21688_20000_rbs_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_rbs/1"/>
+        <sbol:displayId>P21688_20000_rbs_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_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/P21688_20000_gene/P21688_20000_cds_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds/1"/>
+        <sbol:displayId>P21688_20000_cds_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_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/P21688_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/P21688_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/P21688_20000_gene/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_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/P21688_20000_gene/constraint_1/1">
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_2"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds/1">
+    <sbol:displayId>P21688_20000_cds</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_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/P21688_30000_gene/1">
+    <sbol:displayId>P21688_30000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_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/P21688_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/P21688_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/P21688_30000_gene/P21688_30000_rbs_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs/1"/>
+        <sbol:displayId>P21688_30000_rbs_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_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/P21688_30000_gene/P21688_30000_cds_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_cds/1"/>
+        <sbol:displayId>P21688_30000_cds_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_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/P21688_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/P21688_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/P21688_30000_gene/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_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/P21688_30000_gene/constraint_1/1">
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_3_prime_assembly_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_2"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/1">
+    <sbol:displayId>P21683_30000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_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:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:version>1</sbol:version>
+    <sbol:component>
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