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‎.gitignore‎

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/dist/
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/static/
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/templates/
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.idea/
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*.dmg
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*.bin
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src/ml_sbo/models/**

‎README_Enhance.md‎

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# SBOannotator
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<img align="right" src="SBOannotator_logo.png" alt="drawing" width="250"/>
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**SBOannotator: a Python tool for the automated assignment of Systems Biology Ontology terms**
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[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=plastic)](http://opensource.org/licenses/LGPL-3.0)
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[![Latest version](https://img.shields.io/badge/Latest_version-3.0.1-brightgreen.svg?style=plastic)](https://github.com/draeger-lab/SBOannotator/releases/)
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![Code Size](https://img.shields.io/github/languages/code-size/draeger-lab/SBOannotator.svg?style=plastic)
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[![PyPI version](https://badge.fury.io/py/SBOannotator.svg)](https://badge.fury.io/py/SBOannotator)
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![PyPI - Format](https://img.shields.io/pypi/format/SBOannotator)
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[![PyPI downloads](https://img.shields.io/pypi/dm/SBOannotator.svg)](https://pypistats.org/packages/SBOannotator)
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[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtad437-blue.svg?style=plastic)](https://doi.org/10.1093/bioinformatics/btad437)
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Developers : [Nantia Leonidou](https://github.com/NantiaL) & Elisabeth Fritze& Jiahui Hu
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___________________________________________________________________________________________________________
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### Overview
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This project transforms SBOannotator from a static, hard-coded tool into a dynamic, intelligent system for annotating Systems Biology Ontology (SBO) terms in SBML models. The enhanced system integrates real-time SBO term retrieval, multiple enzymology data sources, and LLM-assisted annotation—significantly improving accuracy and usability while preserving the core rule-based strengths. A standalone desktop GUI with interactive visualization makes powerful annotation capabilities accessible to a broader community of systems biology researchers.
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The system delivers three key innovations:
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Automated GitHub integration for real-time SBO file updates;
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A three-layer rule-based annotation workflow;
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A deep-learning classifier achieving 94% accuracy across 42 biochemical reaction classes.
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### Desktop App
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+ Mac: download dmg which is saved in the root directory:`sboannotator.dmg`
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If ERROR occurs, input command in terminal to bypass security check:
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`sudo xattr -r -d com.apple.quarantine /Applications/main.app`
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!But it only can finish rule based annotation because of complex dependencies and direcotory operation with llm.
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### Input data
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+ an SBML document
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+ an sbo terms (.json or obo)(optional)
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### Outputs
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+ Rule Based Enhanced Annotated libSBML model
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+ LLM Annototed libSBML model
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+ Uptodate SBO terms (.json)
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### Usage
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This tool has the following dependencies:
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python >=3.9.6
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Packages:
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sqlite3
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libsbml
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collections
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requests
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json
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time
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-`pip install -r requirements.txt`
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run `python main.py` in the command line within the project folder.
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If ERROR occurs, check the current version of Python:
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- `python --version'`
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- `conda install python>=3.9.6`
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### Exemplary models and results
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The folder `models/Customer_Models` contains a models as it were downloaded from
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the BiGG database.
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The annotated models after using the Rule based SBOannotator and target reaction filtered for llm are listed in the folder named `models/Enhanced_Annotated_Models`.
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The annotated models after using the LLM recommendationi are listed in the models/LLM_Annotated_Models

‎models/Annotated_Models/RECON1_SBOannotated.xml‎

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‎models/Annotated_Models/Recon3D_SBOannotated.xml‎

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‎models/Annotated_Models/TestModel_SBOannotated.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" sboTerm="SBO:0000693" level="3" version="1" fbc:required="false">
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<model metaid="TestModel" id="TestModel" name="AKGDm Test Model" substanceUnits="mole" timeUnits="hour" extentUnits="mole">
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<listOfUnitDefinitions>
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<unitDefinition id="mmol_per_gDW_per_hr">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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<unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
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<unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
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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 sboTerm="SBO:0000290" id="c" name="cytosol" spatialDimensions="3" size="1" constant="true"/>
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<compartment sboTerm="SBO:0000290" id="m" name="mitochondria" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species metaid="M_akg_m" sboTerm="SBO:0000247" id="M_akg_m" name="2-Oxoglutarate" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_coa_m" sboTerm="SBO:0000247" id="M_coa_m" name="Coenzyme A" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_nad_m" sboTerm="SBO:0000247" id="M_nad_m" name="Nicotinamide adenine dinucleotide" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_co2_m" sboTerm="SBO:0000247" id="M_co2_m" name="CO2" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_nadh_m" sboTerm="SBO:0000247" id="M_nadh_m" name="Nicotinamide adenine dinucleotide - reduced" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_succoa_m" sboTerm="SBO:0000247" id="M_succoa_m" name="Succinyl-CoA" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/>
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<parameter sboTerm="SBO:0000626" id="cobra_default_ub" value="1000" constant="true"/>
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<parameter sboTerm="SBO:0000626" id="cobra_0_bound" value="0" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction metaid="R_AKGDm" sboTerm="SBO:0000399" id="R_AKGDm" name="2-oxoglutarate dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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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="#R_AKGDm">
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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08094"/>
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</rdf:Bag>
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</bqbiol:is>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfReactants>
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<speciesReference species="M_akg_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_coa_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_nad_m" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="M_co2_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<fbc:geneProductAssociation>
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<fbc:and>
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<fbc:geneProductRef fbc:geneProduct="G_100689437"/>
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<fbc:geneProductRef fbc:geneProduct="G_100758466"/>
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<fbc:or>
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<fbc:geneProductRef fbc:geneProduct="G_100764862"/>
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<fbc:geneProductRef fbc:geneProduct="G_100769436"/>
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</fbc:or>
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</fbc:and>
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</fbc:geneProductAssociation>
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</reaction>
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</listOfReactions>
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<fbc:listOfObjectives fbc:activeObjective="obj">
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<fbc:objective fbc:id="obj" fbc:type="maximize">
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<fbc:listOfFluxObjectives>
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<fbc:fluxObjective fbc:reaction="R_AKGDm" fbc:coefficient="1"/>
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</fbc:listOfFluxObjectives>
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</fbc:objective>
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</fbc:listOfObjectives>
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<fbc:listOfGeneProducts>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100689437" fbc:name="hypothetical gene 1" fbc:label="gene_100689437"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100758466" fbc:name="hypothetical gene 2" fbc:label="gene_100758466"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100764862" fbc:name="hypothetical gene 3" fbc:label="gene_100764862"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100769436" fbc:name="hypothetical gene 4" fbc:label="gene_100769436"/>
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</fbc:listOfGeneProducts>
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</model>
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</sbml>

‎models/Annotated_Models/TestModel_SBOannotated_enhanced.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" sboTerm="SBO:0000693" level="3" version="1" fbc:required="false">
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<model metaid="TestModel" id="TestModel" name="AKGDm Test Model" substanceUnits="mole" timeUnits="hour" extentUnits="mole">
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<listOfUnitDefinitions>
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<unitDefinition id="mmol_per_gDW_per_hr">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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<unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
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<unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
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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 sboTerm="SBO:0000290" id="c" name="cytosol" spatialDimensions="3" size="1" constant="true"/>
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<compartment sboTerm="SBO:0000290" id="m" name="mitochondria" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species metaid="M_akg_m" sboTerm="SBO:0000247" id="M_akg_m" name="2-Oxoglutarate" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_coa_m" sboTerm="SBO:0000247" id="M_coa_m" name="Coenzyme A" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_nad_m" sboTerm="SBO:0000247" id="M_nad_m" name="Nicotinamide adenine dinucleotide" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_co2_m" sboTerm="SBO:0000247" id="M_co2_m" name="CO2" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_nadh_m" sboTerm="SBO:0000247" id="M_nadh_m" name="Nicotinamide adenine dinucleotide - reduced" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species metaid="M_succoa_m" sboTerm="SBO:0000247" id="M_succoa_m" name="Succinyl-CoA" compartment="m" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/>
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<parameter sboTerm="SBO:0000626" id="cobra_default_ub" value="1000" constant="true"/>
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<parameter sboTerm="SBO:0000626" id="cobra_0_bound" value="0" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction metaid="R_AKGDm" sboTerm="SBO:0000399" id="R_AKGDm" name="2-oxoglutarate dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
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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="#R_AKGDm">
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<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08094"/>
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</rdf:Bag>
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</bqbiol:is>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfReactants>
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<speciesReference species="M_akg_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_coa_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_nad_m" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="M_co2_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/>
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<speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<fbc:geneProductAssociation>
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<fbc:and>
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<fbc:geneProductRef fbc:geneProduct="G_100689437"/>
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<fbc:geneProductRef fbc:geneProduct="G_100758466"/>
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<fbc:or>
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<fbc:geneProductRef fbc:geneProduct="G_100764862"/>
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<fbc:geneProductRef fbc:geneProduct="G_100769436"/>
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</fbc:or>
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</fbc:and>
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</fbc:geneProductAssociation>
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</reaction>
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</listOfReactions>
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<fbc:listOfObjectives fbc:activeObjective="obj">
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<fbc:objective fbc:id="obj" fbc:type="maximize">
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<fbc:listOfFluxObjectives>
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<fbc:fluxObjective fbc:reaction="R_AKGDm" fbc:coefficient="1"/>
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</fbc:listOfFluxObjectives>
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</fbc:objective>
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</fbc:listOfObjectives>
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<fbc:listOfGeneProducts>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100689437" fbc:name="hypothetical gene 1" fbc:label="gene_100689437"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100758466" fbc:name="hypothetical gene 2" fbc:label="gene_100758466"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100764862" fbc:name="hypothetical gene 3" fbc:label="gene_100764862"/>
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<fbc:geneProduct sboTerm="SBO:0000243" fbc:id="G_100769436" fbc:name="hypothetical gene 4" fbc:label="gene_100769436"/>
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</fbc:listOfGeneProducts>
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</model>
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</sbml>

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