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JR-1991JR-1991
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add test cases
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‎tests/data/expected_omex_content.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
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<model name="Test">
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<annotation>
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<enzymeml:data xmlns:enzymeml="https://www.enzymeml.org/v2" file="data.tsv">
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<enzymeml:measurement id="m0" name="m0" timeUnit="u1">
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<enzymeml:conditions>
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<enzymeml:ph value="7.0"/>
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<enzymeml:temperature value="298.15" unit="u3"/>
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</enzymeml:conditions>
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<enzymeml:speciesData species="s0" unit="u2" type="CONCENTRATION"/>
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<enzymeml:speciesData species="s1" value="10.0" unit="u2" type="CONCENTRATION"/>
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</enzymeml:measurement>
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<enzymeml:measurement id="m1" name="m1" timeUnit="u1">
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<enzymeml:conditions>
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<enzymeml:ph value="7.0"/>
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<enzymeml:temperature value="298.15" unit="u3"/>
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</enzymeml:conditions>
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<enzymeml:speciesData species="s0" unit="u2" type="CONCENTRATION"/>
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<enzymeml:speciesData species="s1" value="10.0" unit="u2" type="CONCENTRATION"/>
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</enzymeml:measurement>
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</enzymeml:data>
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</annotation>
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<listOfUnitDefinitions>
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<unitDefinition id="u0" name="ml">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000098">
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="-3"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u2" name="mmol / l">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000063">
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3"/>
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<unit kind="litre" exponent="-1" scale="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u1" name="s">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000010">
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfUnits>
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<unit kind="second" exponent="1" scale="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u3" name="K">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000012">
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfUnits>
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<unit kind="kelvin" exponent="1" scale="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u4" name="1 / s">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000010">
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfUnits>
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<unit kind="second" exponent="-1" scale="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="v0" name="Vessel 1" size="10" units="u0" constant="true">
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<annotation>
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<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Vessel/abc02182-675a-4fd7-b067-9f376f17b874">
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<schema:name>Vessel 1</schema:name>
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<OBO:OBI_0002139 rdf:datatype="http://www.w3.org/2001/XMLSchema#double">10.0</OBO:OBI_0002139>
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Vessel"/>
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<rdf:type rdf:resource="http://purl.obolibrary.org/obo/OBI_0400081"/>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species sboTerm="SBO:0000252" id="p0" name="Enzyme" compartment="v0" constant="false">
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<annotation>
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<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Protein/487be0d2-e325-4f0b-857b-3bd8d54c4003">
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<schema:name>Enzyme</schema:name>
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<OBO:GSSO_007262>MTEY</OBO:GSSO_007262>
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<OBO:OBI_0100026>E.coli</OBO:OBI_0100026>
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Protein"/>
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<rdf:type rdf:resource="https://schema.org/Protein"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:protein xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:ecnumber>1.1.1.1</enzymeml:ecnumber>
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<enzymeml:organism>E.coli</enzymeml:organism>
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<enzymeml:organismTaxId>12345</enzymeml:organismTaxId>
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<enzymeml:sequence>MTEY</enzymeml:sequence>
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</enzymeml:protein>
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</annotation>
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</species>
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<species sboTerm="SBO:0000296" id="c0" name="Enzyme-Substrate Complex" constant="true">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Complex/2f52086d-d7a8-4a2d-870b-bd6bafd91504">
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<schema:name>Enzyme-Substrate Complex</schema:name>
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Complex"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:complex xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:participants>p0</enzymeml:participants>
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<enzymeml:participants>s0</enzymeml:participants>
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</enzymeml:complex>
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</annotation>
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</species>
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<species sboTerm="SBO:0000247" id="s0" name="Substrate" compartment="v0" initialConcentration="0" hasOnlySubstanceUnits="false" constant="false">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/551e35d3-ae18-490d-b4a7-003fcd28f446">
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<schema:name>Substrate</schema:name>
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:smallMolecule xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:inchiKey>QTBSBXVTEAMEQO-UHFFFAOYSA-N</enzymeml:inchiKey>
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<enzymeml:smiles>CC(=O)O</enzymeml:smiles>
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</enzymeml:smallMolecule>
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</annotation>
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</species>
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<species sboTerm="SBO:0000247" id="s1" name="Product" compartment="v0" initialConcentration="10" hasOnlySubstanceUnits="false" constant="false">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/1a93b3f8-ce94-429d-975b-ff6a837b0424">
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<schema:name>Product</schema:name>
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:smallMolecule xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:inchiKey>QTBSBXVTEAMEQO-UHFFFAOYSA-N</enzymeml:inchiKey>
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<enzymeml:smiles>CC(=O)O</enzymeml:smiles>
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</enzymeml:smallMolecule>
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</annotation>
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="kcat" name="kcat" units="u4" constant="true">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/2872b6d6-191f-4bc4-a36a-130eb4534837">
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:parameter xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:lowerBound>0.0</enzymeml:lowerBound>
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<enzymeml:upperBound>100.0</enzymeml:upperBound>
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<enzymeml:stdDeviation>0.1</enzymeml:stdDeviation>
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</enzymeml:parameter>
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</annotation>
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</parameter>
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<parameter id="K_m" name="K_m" units="u2" constant="true">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/31e315d7-8e87-4ef9-9ca4-1e9e08f2ded7">
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:parameter xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:lowerBound>0.0</enzymeml:lowerBound>
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<enzymeml:upperBound>100.0</enzymeml:upperBound>
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<enzymeml:stdDeviation>0.1</enzymeml:stdDeviation>
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</enzymeml:parameter>
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</annotation>
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</parameter>
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<parameter id="E_tot" name="E_tot" units="u2" constant="true">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/d49325e0-8483-469a-9d6d-1bcadac2bb98">
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<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
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</rdf:Description>
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</rdf:RDF>
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<enzymeml:parameter xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:lowerBound>0.0</enzymeml:lowerBound>
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<enzymeml:upperBound>100.0</enzymeml:upperBound>
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<enzymeml:stdDeviation>0.1</enzymeml:stdDeviation>
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</enzymeml:parameter>
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</annotation>
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</parameter>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="E_tot">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<cn type="integer"> 100 </cn>
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</math>
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</initialAssignment>
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</listOfInitialAssignments>
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<listOfRules>
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<rateRule variable="s1">
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<annotation>
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<enzymeml:variables xmlns:enzymeml="https://www.enzymeml.org/v2">
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<enzymeml:variable id="s0" name="s0" symbol="s0"/>
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</enzymeml:variables>
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</annotation>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<divide/>
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<apply>
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<times/>
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<ci> E_tot </ci>
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<ci> kcat </ci>
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<ci> s0 </ci>
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</apply>
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<apply>
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<plus/>
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<ci> K_m </ci>
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<ci> s0 </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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</listOfRules>
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</model>
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</sbml>

‎tests/data/expected_omex_data.tsv

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time s0 s1 id
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0.0 0.0 10.0 m0
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1.0 1.0 9.0 m0
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2.0 2.0 8.0 m0
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3.0 3.0 7.0 m0
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4.0 4.0 6.0 m0
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5.0 5.0 5.0 m0
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6.0 6.0 4.0 m0
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7.0 7.0 3.0 m0
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8.0 8.0 2.0 m0
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9.0 9.0 1.0 m0
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10.0 10.0 0.0 m0
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0.0 0.0 10.0 m1
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1.0 1.0 9.0 m1
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2.0 2.0 8.0 m1
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3.0 3.0 7.0 m1
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4.0 4.0 6.0 m1
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5.0 5.0 5.0 m1
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6.0 6.0 4.0 m1
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7.0 7.0 3.0 m1
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8.0 8.0 2.0 m1
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9.0 9.0 1.0 m1
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10.0 10.0 0.0 m1

‎tests/data/test.omex

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