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

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 15 Dec 2021 13:59:04 +0000
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-1:000000000000 0:481f7c35323d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <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">
3 <model metaid="ab7a7ab71c6ccfe1bb89180d9a6fb504a8ea4784c1ace396ce99cb6892d1b81e" id="RP_model_003_0261" name="003_0261" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
5 <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
6 <annotation>
7 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
8 <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
9 <bqbiol:is>
10 <rdf:Bag>
11 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag>
19 </bqbiol:is>
20 </rdf:Description>
21 </rdf:RDF>
22 </annotation>
23 </compartment>
24 </listOfCompartments>
25 <listOfSpecies>
26 <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
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37 <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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47 <brsynth:units value="kilojoule / mole"/>
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49 </brsynth:brsynth>
50 </rdf:BRSynth>
51 </rdf:RDF>
52 </annotation>
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54 <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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65 <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"/>
66 <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
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72 </brsynth:fba_fraction_shadow_price>
73 <brsynth:thermo_standard_dg_formation>
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75 <brsynth:units value="kilojoule / mole"/>
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77 </brsynth:brsynth>
78 </rdf:BRSynth>
79 </rdf:RDF>
80 </annotation>
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83 <annotation>
84 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
85 <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
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91 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
92 <brsynth:smiles/>
93 <brsynth:inchi/>
94 <brsynth:inchikey/>
95 <brsynth:fba_biomass_shadow_price>
96 <brsynth:value value="None"/>
97 </brsynth:fba_biomass_shadow_price>
98 <brsynth:fba_fraction_shadow_price>
99 <brsynth:value value="None"/>
100 </brsynth:fba_fraction_shadow_price>
101 <brsynth:thermo_standard_dg_formation>
102 <brsynth:value value="-2256.1898491337233"/>
103 <brsynth:units value="kilojoule / mole"/>
104 </brsynth:thermo_standard_dg_formation>
105 </brsynth:brsynth>
106 </rdf:BRSynth>
107 </rdf:RDF>
108 </annotation>
109 </species>
110 <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="MNXM34" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
111 <annotation>
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113 <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
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121 <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)"/>
122 <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
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129 <brsynth:thermo_standard_dg_formation>
130 <brsynth:value value="-1607.8991259717538"/>
131 <brsynth:units value="kilojoule / mole"/>
132 </brsynth:thermo_standard_dg_formation>
133 </brsynth:brsynth>
134 </rdf:BRSynth>
135 </rdf:RDF>
136 </annotation>
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138 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
139 <annotation>
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142 <bqbiol:is>
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149 <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"/>
150 <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
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157 <brsynth:thermo_standard_dg_formation>
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159 <brsynth:units value="kilojoule / mole"/>
160 </brsynth:thermo_standard_dg_formation>
161 </brsynth:brsynth>
162 </rdf:BRSynth>
163 </rdf:RDF>
164 </annotation>
165 </species>
166 <species metaid="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
167 <annotation>
168 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
169 <rdf:Description rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
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174 <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
175 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
176 <brsynth:smiles/>
177 <brsynth:inchi/>
178 <brsynth:inchikey/>
179 <brsynth:fba_biomass_shadow_price>
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181 </brsynth:fba_biomass_shadow_price>
182 <brsynth:fba_fraction_shadow_price>
183 <brsynth:value value="None"/>
184 </brsynth:fba_fraction_shadow_price>
185 <brsynth:thermo_standard_dg_formation>
186 <brsynth:value value="-2172.1728715236113"/>
187 <brsynth:units value="kilojoule / mole"/>
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189 </brsynth:brsynth>
190 </rdf:BRSynth>
191 </rdf:RDF>
192 </annotation>
193 </species>
194 <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
195 <annotation>
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202 <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
203 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
204 <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]"/>
205 <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)"/>
206 <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
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210 <brsynth:fba_fraction_shadow_price>
211 <brsynth:value value="None"/>
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213 <brsynth:thermo_standard_dg_formation>
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234 <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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241 <brsynth:thermo_standard_dg_formation>
242 <brsynth:value value="-1966.8036657706114"/>
243 <brsynth:units value="kilojoule / mole"/>
244 </brsynth:thermo_standard_dg_formation>
245 </brsynth:brsynth>
246 </rdf:BRSynth>
247 </rdf:RDF>
248 </annotation>
249 </species>
250 </listOfSpecies>
251 <listOfParameters>
252 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
253 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
254 </listOfParameters>
255 <listOfReactions>
256 <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">
257 <annotation>
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260 <bqbiol:is>
261 <rdf:Bag>
262 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.92"/>
263 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.85"/>
264 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.84"/>
265 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.31"/>
266 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.81"/>
267 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.88"/>
268 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.-"/>
269 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/>
270 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
271 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.68"/>
272 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.10"/>
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274 </bqbiol:is>
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279 <brsynth:rp2_transfo_id value="TRS_0_2_742"/>
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291 <brsynth:MNXR112247/>
292 <brsynth:MNXR116653/>
293 <brsynth:MNXR100621/>
294 <brsynth:MNXR99634/>
295 <brsynth:MNXR112069/>
296 <brsynth:MNXR99650/>
297 <brsynth:MNXR109677/>
298 <brsynth:MNXR113141/>
299 <brsynth:MNXR105052/>
300 <brsynth:MNXR109713/>
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304 <brsynth:MNXR112250/>
305 <brsynth:MNXR112251/>
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308 <brsynth:MNXR117266/>
309 <brsynth:MNXR139515/>
310 <brsynth:MNXR139637/>
311 <brsynth:MNXR112249/>
312 <brsynth:MNXR116655/>
313 <brsynth:MNXR103150/>
314 <brsynth:MNXR112248/>
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331 <brsynth:units value="kilojoule / mole"/>
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340 <brsynth:error value="2.9407032504945367"/>
341 <brsynth:units value="kilojoule / mole"/>
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343 <brsynth:thermo_dG>
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345 <brsynth:error value="2.9407032504945367"/>
346 <brsynth:units value="kilojoule / mole"/>
347 </brsynth:thermo_dG>
348 </brsynth:brsynth>
349 </rdf:BRSynth>
350 </rdf:RDF>
351 </annotation>
352 <listOfReactants>
353 <speciesReference species="MNXM34" stoichiometry="1" constant="true"/>
354 <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
355 </listOfReactants>
356 <listOfProducts>
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360 </reaction>
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400 <brsynth:error value="11.000567449695138"/>
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419 </rdf:BRSynth>
420 </rdf:RDF>
421 </annotation>
422 <listOfReactants>
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424 </listOfReactants>
425 <listOfProducts>
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429 </reaction>
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622 </groups:listOfMembers>
623 </groups:group>
624 </groups:listOfGroups>
625 </model>
626 </sbml>