annotate test-data/pathway.xml @ 0:481f7c35323d draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

<?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="ab7a7ab71c6ccfe1bb89180d9a6fb504a8ea4784c1ace396ce99cb6892d1b81e" id="RP_model_003_0261" name="003_0261" 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="_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>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
              <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]"/>
                <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)"/>
                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
                <brsynth:fba_biomass_shadow_price>
                  <brsynth:value value="-0.4636266049503492"/>
                </brsynth:fba_biomass_shadow_price>
                <brsynth:fba_fraction_shadow_price>
                  <brsynth:value value="-0.9959432048681541"/>
                </brsynth:fba_fraction_shadow_price>
                <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>
      </species>
      <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="-0.46174576679639245"/>
                </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>
            </rdf:Description>
            <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="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="MNXM34" 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="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
              <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])[H]"/>
                <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
                <brsynth:inchikey value="VWFJDQUYCIWHTN-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="-1607.8991259717538"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_standard_dg_formation>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_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="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
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              <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="-0.46174576679639245"/>
                </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="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" 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="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
              <bqbiol:is>
                <rdf:Bag/>
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            </rdf:Description>
            <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
              <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="-2172.1728715236113"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_standard_dg_formation>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <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/>
              </bqbiol:is>
            </rdf:Description>
            <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="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/>
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            </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>
    </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/ec-code/2.5.1.92"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.85"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.84"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.31"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.81"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.88"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.-"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.68"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.10"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
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                  <brsynth:MNXR139637/>
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                <brsynth:fba_fraction>
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                <brsynth:thermo_dG>
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                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="MNXM34" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
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                  <brsynth:value value="-153.36328074340173"/>
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                <brsynth:thermo_dG_prime>
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                <brsynth:thermo_dG>
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                </brsynth:thermo_dG>
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            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
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        <listOfReactants>
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</sbml>