Mercurial > repos > tduigou > rpcompletion

comparison test-data/rp_001_0001.xml @ 0:98d925a75257 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 23 Nov 2021 13:45:45 +0000
parents
children b8242cf18cc0
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-1:000000000000 0:98d925a75257
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="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" 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>
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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)"/>
38 <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
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73 <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)"/>
74 <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
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91 <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"/>
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107 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
108 <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
109 <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
110 <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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116 <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="dimethylallyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
117 <annotation>
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120 <bqbiol:is>
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125 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
126 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
127 <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)"/>
128 <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>
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130 </rdf:BRSynth>
131 </rdf:RDF>
132 </annotation>
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134 <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
135 <annotation>
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145 <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"/>
146 <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
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152 <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
153 <annotation>
154 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
155 <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
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165 </brsynth:brsynth>
166 </rdf:BRSynth>
167 </rdf:RDF>
168 </annotation>
169 </species>
170 </listOfSpecies>
171 <listOfParameters>
172 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
173 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
174 </listOfParameters>
175 <listOfReactions>
176 <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
177 <annotation>
178 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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180 <bqbiol:is>
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189 <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
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203 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
204 <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/>
205 </listOfReactants>
206 <listOfProducts>
207 <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
208 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
209 </listOfProducts>
210 </reaction>
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212 <annotation>
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218 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/>
219 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/>
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223 <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
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226 <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
227 <brsynth:rule_ids>
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229 </brsynth:rule_ids>
230 <brsynth:tmpl_rxn_ids>
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232 <brsynth:MNXR111499/>
233 <brsynth:MNXR113543/>
234 <brsynth:MNXR118024/>
235 <brsynth:MNXR139549/>
236 </brsynth:tmpl_rxn_ids>
237 <brsynth:rule_score value="0.5518755963407151"/>
238 <brsynth:idx_in_path value="2"/>
239 </brsynth:brsynth>
240 </rdf:BRSynth>
241 </rdf:RDF>
242 </annotation>
243 <listOfReactants>
244 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
245 </listOfReactants>
246 <listOfProducts>
247 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
248 <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
249 </listOfProducts>
250 </reaction>
251 <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
252 <annotation>
253 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
254 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
255 <bqbiol:is>
256 <rdf:Bag>
257 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
258 </rdf:Bag>
259 </bqbiol:is>
260 </rdf:Description>
261 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
262 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
263 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].[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.O=P(O)(O)OP(=O)(O)O"/>
264 <brsynth:rp2_transfo_id value="TRS_0_2_739"/>
265 <brsynth:rule_ids>
266 <brsynth:RR-02-90bcfd187709eb1b-14-F/>
267 </brsynth:rule_ids>
268 <brsynth:tmpl_rxn_ids>
269 <brsynth:MNXR132232/>
270 </brsynth:tmpl_rxn_ids>
271 <brsynth:rule_score value="0.5706379442030705"/>
272 <brsynth:idx_in_path value="1"/>
273 </brsynth:brsynth>
274 </rdf:BRSynth>
275 </rdf:RDF>
276 </annotation>
277 <listOfReactants>
278 <speciesReference species="MNXM132" stoichiometry="1" constant="true"/>
279 <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
280 </listOfReactants>
281 <listOfProducts>
282 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
283 <speciesReference species="MNXM11" stoichiometry="3" constant="true"/>
284 </listOfProducts>
285 </reaction>
286 </listOfReactions>
287 <groups:listOfGroups>
288 <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
289 <annotation>
290 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
291 <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
292 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
293 <brsynth:global_score value="-1"/>
294 </brsynth:brsynth>
295 </rdf:BRSynth>
296 </rdf:RDF>
297 </annotation>
298 <groups:listOfMembers>
299 <groups:member groups:idRef="rxn_1"/>
300 <groups:member groups:idRef="rxn_2"/>
301 <groups:member groups:idRef="rxn_3"/>
302 </groups:listOfMembers>
303 </groups:group>
304 <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
305 <annotation>
306 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
307 <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
308 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
309 </rdf:BRSynth>
310 </rdf:RDF>
311 </annotation>
312 <groups:listOfMembers>
313 <groups:member groups:idRef="CMPD_0000000001"/>
314 <groups:member groups:idRef="CMPD_0000000003"/>
315 </groups:listOfMembers>
316 </groups:group>
317 <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
318 <annotation>
319 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
320 <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
321 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
322 </rdf:BRSynth>
323 </rdf:RDF>
324 </annotation>
325 <groups:listOfMembers>
326 <groups:member groups:idRef="CMPD_0000000003"/>
327 <groups:member groups:idRef="MNXM83"/>
328 <groups:member groups:idRef="TARGET_0000000001"/>
329 <groups:member groups:idRef="MNXM132"/>
330 <groups:member groups:idRef="CMPD_0000000001"/>
331 </groups:listOfMembers>
332 </groups:group>
333 <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
334 <annotation>
335 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
336 <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
337 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
338 </rdf:BRSynth>
339 </rdf:RDF>
340 </annotation>
341 <groups:listOfMembers>
342 <groups:member groups:idRef="MNXM8975"/>
343 <groups:member groups:idRef="MNXM11"/>
344 <groups:member groups:idRef="MNXM24"/>
345 </groups:listOfMembers>
346 </groups:group>
347 <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
348 <annotation>
349 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
350 <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
351 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
352 </rdf:BRSynth>
353 </rdf:RDF>
354 </annotation>
355 <groups:listOfMembers>
356 <groups:member groups:idRef="MNXM83"/>
357 <groups:member groups:idRef="MNXM11"/>
358 <groups:member groups:idRef="MNXM132"/>
359 </groups:listOfMembers>
360 </groups:group>
361 </groups:listOfGroups>
362 </model>
363 </sbml>