{"MarkerWords":"Genome","ThresholdValue":1,"Steps":"Obtain genome annotation","Group":"Data Collection","UniProtKnowledgeBase":1,"NCBI_Gene":1,"KEGG_Genes":1,"KEGG_Genome":1,"NCBI_Protein":1}
{"MarkerWords":"Candidate;function","ThresholdValue":1,"Steps":"Identify candidate metabolic functions","Group":"Data Collection","KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"BioCyc":1,"MetaCycCompound":1,"MetaCycReaction":1}
{"MarkerWords":"Candidate;reaction","ThresholdValue":1,"Steps":"Identify candidate metabolic reactions","Group":"Data Collection","KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"BioCyc":1,"MetaCycCompound":1,"MetaCycReaction":1,"KEGGREST":1}
{"MarkerWords":"Reconstruction;construction;Assemble;draft","ThresholdValue":0.75,"Steps":"Assemble draft reconstruction","Group":"Draft Reconstruction","COBRA":1,"RAVEN":1,"CarveMe":1,"AuReMe":1,"MetaDraft":1,"ModelSEED":1,"PathwayTools":1,"Merlin":1,"AGORA":1,"COBRApy":1}
{"MarkerWords":"Homology;Blast","ThresholdValue":0.5,"Steps":"Use the phylogenetically close organisms","Group":"Reconstruction Refinement","BLAST":1}
{"MarkerWords":"Experimental;data","ThresholdValue":1,"Steps":"Collect the experimental data","Group":"Reconstruction Refinement","ExperimentOrLiterature":1}
{"MarkerWords":"Substrate;cofactor","ThresholdValue":1,"Steps":"Determine the substrates and cofactors for usage","Group":"Information Analysis","KEGG_Compound":1,"COBRA":1,"RAVEN":1,"BRENDA":1,"minval":1}
{"MarkerWords":"Neutral","ThresholdValue":1,"Steps":"Obtain the neutral molecular formula","Group":"Data Collection","KEGG_Compound":1,"MetaCycCompound":1,"BRENDA":1,"ChEBI":1,"PubChem_Compound":1,"ChEMBL_Compound":1,"Rhea":1}
{"MarkerWords":"Charged","ThresholdValue":1,"Steps":"Determine the charged molecular formula","Group":"Data Collection","KEGG_Compound":1,"MetaCycCompound":1,"BRENDA":1,"ChEBI":1,"PubChem_Compound":1,"ChEMBL_Compound":1,"Rhea":1,"pKa_DB":1,"rsbml":1,"PipelinePilot":1}
{"MarkerWords":"Conservation;mass;charge","ThresholdValue":1,"Steps":"Calculate the reaction stoichiometry","Group":"Data Quality Control","COBRA":1,"RAVEN":1,"CarveMe":1,"AuReMe":1,"MetaDraft":1,"ModelSEED":1,"PathwayTools":1,"Merlin":1,"AGORA":1,"minval":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Directionality;reversibility;irreversible","ThresholdValue":0.3,"Steps":"Determine reaction directionality","Group":"Data Collection","KEGG_Reaction":1,"MetaCycReaction":1}
{"MarkerWords":"Cellular;compartment;localization","ThresholdValue":0.3,"Steps":"Add the cellular compartments information","Group":"Data Collection","UniProtKnowledgeBase":1,"NCBI_Gene":1,"NCBI_Protein":1,"BLAST":1,"BUSCA":1,"PSORT":1,"PASUB":1}
{"MarkerWords":"Subsystem","ThresholdValue":1,"Steps":"Add the subsystem information","Group":"Data Collection","UniProtKnowledgeBase":1,"KEGG_Pathway":1,"MetaCycReaction":1}
{"MarkerWords":"GPR","ThresholdValue":1,"Steps":"Verify gene-protein-reaction associations","Group":"Reconstruction Refinement","KEGG_Genes":1,"KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"MetaCycCompound":1,"MetaCycReaction":1}
{"MarkerWords":"identifier","ThresholdValue":1,"Steps":"Add metabolite identifiers","Group":"Data Collection","KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"COBRA":1,"RAVEN":1,"CarveMe":1,"AuReMe":1,"MetaDraft":1,"ModelSEED":1,"PathwayTools":1,"Merlin":1,"AGORA":1,"ChEBI":1,"PubChem_Compound":1,"PubChem_Substance":1,"STRING":1}
{"MarkerWords":"consistent;identifier;Uniform","ThresholdValue":0.6,"Steps":"Unify metabolite/reaction identifiers","Group":"Information Analysis","KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"ChEBI":1,"PubChem_Compound":1,"PubChem_Substance":1,"STRING":1}
{"MarkerWords":"Confidence;score","ThresholdValue":1,"Steps":"Determine and add the confidence score","Group":"Reconstruction Refinement","COBRA":1,"RAVEN":1,"CarveMe":1,"AuReMe":1,"MetaDraft":1,"ModelSEED":1,"PathwayTools":1,"Merlin":1,"AGORA":1}
{"MarkerWords":"reaction;information;source","ThresholdValue":1,"Steps":"Add reaction information sources","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"Add;note;experiment","ThresholdValue":1,"Steps":"Add notes based on experiments","Group":"Reconstruction Refinement","COBRA":1,"RAVEN":1,"CarveMe":1,"AuReMe":1,"MetaDraft":1,"ModelSEED":1,"Merlin":1,"AGORA":1}
{"MarkerWords":"iteration","ThresholdValue":1,"Steps":"Initial ireration","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"Spontaneous","ThresholdValue":1,"Steps":"Add spontaneous reactions","Group":"Data Curation","KEGG_Pathway":1,"KEGG_Compound":1,"KEGG_Reaction":1,"BRENDA":1}
{"MarkerWords":"Extracellular;periplasmic;transport","ThresholdValue":0.6,"Steps":"Add exracellular transport and periplasmic transport reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"Exchange","ThresholdValue":1,"Steps":"Add exchange reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"Intracellular;transport","ThresholdValue":1,"Steps":"Add intracellular transport reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"Visualization","ThresholdValue":1,"Steps":"Draw the metabolic map","Group":"Reconstruction Refinement","ExperimentOrLiterature":1}
{"MarkerWords":"chemical;composition","ThresholdValue":1,"Steps":"Determine cytochemical compositions","Group":"Reconstruction Refinement","CMR":1}
{"MarkerWords":"amino;acid","ThresholdValue":1,"Steps":"Estimate amino acid contents","Group":"Reconstruction Refinement","ExperimentOrLiterature":1}
{"MarkerWords":"amino;acid;coefficient","ThresholdValue":1,"Steps":"Determine amino acid coefficients","Group":"Information Analysis","CMR":1}
{"MarkerWords":"Nucleotide","ThresholdValue":1,"Steps":"Estimate nucleotide contents","Group":"Reconstruction Refinement","ExperimentOrLiterature":1}
{"MarkerWords":"Nucleotide;Coefficient","ThresholdValue":1,"Steps":"Determine nucleotide coefficients","Group":"Information Analysis","ExperimentOrLiterature":1}
{"MarkerWords":"lipid;content","ThresholdValue":1,"Steps":"Estimate lipid contents","Group":"Reconstruction Refinement","ExperimentOrLiterature":1}
{"MarkerWords":"cofactor;polyamines;vitamin","ThresholdValue":0.5,"Steps":"Estimate cofactor contents","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"ion","ThresholdValue":1,"Steps":"Estimate ion contents","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"GAM","ThresholdValue":1,"Steps":"Determine growth-associated ATP maintenance reactions","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"Biomass","ThresholdValue":1,"Steps":"Add biomass reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"NGAM","ThresholdValue":1,"Steps":"Add no growth-associated ATP maintenance reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"Demand","ThresholdValue":1,"Steps":"Add demand reactions","Group":"Data Curation","ExperimentOrLiterature":1}
{"MarkerWords":"Sink","ThresholdValue":1,"Steps":"Add sink reactions","Group":"Data Curation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Growth;medium","ThresholdValue":1,"Steps":"Determine growth medium requiremnets","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1}
{"MarkerWords":"COBRA","ThresholdValue":1,"Steps":"Use COBRA","Group":"Reconstruction Refinement","COBRA":1,"RAVEN":1,"COBRApy":1,"minval":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Matlab","ThresholdValue":1,"Steps":"Load reconstructions into Matlab","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Verify;matrix","ThresholdValue":1,"Steps":"Verify matrix","Group":"Data Quality Control","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Objective;function","ThresholdValue":1,"Steps":"Set objective functions","Group":"Data Curation","COBRA":1,"RAVEN":1,"COBRApy":1,"minval":1}
{"MarkerWords":"Simulation;constraint","ThresholdValue":1,"Steps":"Set simulaton constraints","Group":"Data Curation","COBRA":1,"RAVEN":1,"COBRApy":1,"minval":1}
{"MarkerWords":"Check;unbalanced","ThresholdValue":1,"Steps":"Check for stoichiometrically unbalanced reactions","Group":"Data Quality Control","COBRA":1,"COBRApy":1,"minval":1,"g2f":1}
{"MarkerWords":"Evaluate;unbalanced","ThresholdValue":1,"Steps":"Evaluate stoichiometrically unbalanced reactions","Group":"Data Quality Control","COBRA":1,"COBRApy":1,"g2f":1}
{"MarkerWords":"terminal;dead;end","ThresholdValue":0.6,"Steps":"Identify terminal metabolites","Group":"Information Analysis","COBRA":1,"COBRApy":1,"g2f":1}
{"MarkerWords":"candidate;fill;gap","ThresholdValue":1,"Steps":"Identify candidate reactions to fill gaps","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"fill;gap","ThresholdValue":1,"Steps":"Add gap reactions to fill gaps","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"note;reference;dead;end","ThresholdValue":0.5,"Steps":"Add notes and references to terminal metabolites","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"missing;exchange","ThresholdValue":1,"Steps":"Add missing exchange reactions","Group":"Data Curation","COBRA":1,"COBRApy":1}
{"MarkerWords":"simulation;condition;constraint","ThresholdValue":1,"Steps":"Set missing exchange constraints for a simulation condition","Group":"Data Curation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Test;Type;III","ThresholdValue":1,"Steps":"Test for Type III pathways","Group":"Data Quality Control","COBRA":1,"COBRApy":1}
{"MarkerWords":"Discover;Type;III","ThresholdValue":1,"Steps":"Discover Type III pathways","Group":"Information Analysis","ManualPlanning":1}
{"MarkerWords":"Identify;Type;III","ThresholdValue":1,"Steps":"Identify Type III pathways","Group":"Information Analysis","COBRA":1,"COBRApy":1,"minval":1,"g2f":1}
{"MarkerWords":"Type;III;directionality","ThresholdValue":1,"Steps":"Analyze reactions direactionality in Type III","Group":"Information Analysis","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"network;gap","ThresholdValue":1,"Steps":"Recompute networks gaps","Group":"Data Quality Control","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Biomass;metabolite;component","ThresholdValue":1,"Steps":"Obtain biomass reaction metabolites","Group":"Information Analysis","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Biomass;precursor;metabolite;demand;function","ThresholdValue":1,"Steps":"Add demand reactions for biomass reaction","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Biomass;objective;function","ThresholdValue":1,"Steps":"Set objective functions of biomass reactions","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Maximize;objective;function;max","ThresholdValue":0.75,"Steps":"Maximize objective functions","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Identify;main;reaction;biomass;component","ThresholdValue":0.8,"Steps":"Identify the main reactions","Group":"Model Evaluation","ExperimentOrLiterature":1}
{"MarkerWords":"Growth;Media;Simulation","ThresholdValue":1,"Steps":"Sitimulate the multi-growth media","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Collection;secretion;growth;condition","ThresholdValue":1,"Steps":"Collect secretions and growth conditions","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Secretion;constraint","ThresholdValue":1,"Steps":"Set the simulation constraints for the single secretion","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Secretion;objective;function","ThresholdValue":1,"Steps":"Set the objective functions of the single secretion","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Secretion;maximization;objective;function;max","ThresholdValue":0.8,"Steps":"Maximize the objective functions of the single secretion","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Multiple;secretion;constraint","ThresholdValue":0.6,"Steps":"Set the constraints of multiple secretions","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Validate;model","ThresholdValue":1,"Steps":"Validate the model","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Addition;secretion;add","ThresholdValue":0.6,"Steps":"Add secretion reactions","Group":"Data Curation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Multi;Secretion;objective;function","ThresholdValue":1,"Steps":"Set the objective functions of multiple secretions","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Multi;Secretion;max;objective;function","ThresholdValue":1,"Steps":"Maximize the objective reactions of multiple secreations","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Simulate;rich;medium","ThresholdValue":0.6,"Steps":"Simulate rich media","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Blocking;blocked","ThresholdValue":0.5,"Steps":"Check for blocked reactions","Group":"Information Analysis","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Blocking;fill;gap;blocked","ThresholdValue":0.75,"Steps":"Fill gaps by blocked reactions","Group":"Data Curation","ManualPlanning":1}
{"MarkerWords":"Simulate;single;gene;knockout;deletion","ThresholdValue":1,"Steps":"Simulate the single-gene deletion","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"validation;model;single;gene","ThresholdValue":1,"Steps":"Validate the single-gene deletion model","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1}
{"MarkerWords":"simulation;condition","ThresholdValue":1,"Steps":"Set the simulation conditions","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"single;reaction;knockout","ThresholdValue":1,"Steps":"Simulate the single-reaction deletion","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"single;Reaction;validation;model","ThresholdValue":1,"Steps":"Validate the single-reaction deletion model","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Multimedia;verification;model","ThresholdValue":1,"Steps":"Validate the multi-media model (fast enough)","Group":"Model Evaluation","COBRA":1,"COBRApy":1,"rsbml":1,"Sybil":1}
{"MarkerWords":"Determine;model;quality","ThresholdValue":1,"Steps":"Determine model quality","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Multimedia;max;objective;function","ThresholdValue":1,"Steps":"Maximize the objective multiple media","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Reduce;cost;shadow","ThresholdValue":0.6,"Steps":"Determine the reduced cost associated with network reactions when optimizing for objective function.","Group":"Model Evaluation","ManualPlanning":1}
{"MarkerWords":"Multimedia;Verification;Model","ThresholdValue":1,"Steps":"Validate multiple-media model (too fast)","Group":"Model Evaluation","ManualPlanning":1}
{"MarkerWords":"Multimedia;Verification;Model","ThresholdValue":1,"Steps":"Use single-reaction deletion to identify single reactions that may enable the model to grow too fast","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"Determining;biomass;metabolite;integrity","ThresholdValue":0.75,"Steps":"Validate the integrity of bimass metabolites","Group":"Reconstruction Refinement","ManualPlanning":1}
{"MarkerWords":"Shuttle","ThresholdValue":1,"Steps":"Identify shuttling reactions","Group":"Reconstruction Refinement","COBRA":1,"COBRApy":1}
{"MarkerWords":"iteration","ThresholdValue":1,"Steps":"Last iteration","Group":"Data Curation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Identify;excessive;growth","ThresholdValue":1,"Steps":"Identify excessive growth","Group":"Model Evaluation","COBRA":1,"COBRApy":1}
{"MarkerWords":"Reduce;costs;shadow","ThresholdValue":0.6,"Steps":"Use reduced cost analysis to identify those reactions that can reduce the growth rate","Group":"Information Analysis","ManualPlanning":1}
{"MarkerWords":"Output file format","ThresholdValue":1,"Steps":"Output files","Group":"Reconstruction Output"}
{"MarkerWords":"Annotation;gap","ThresholdValue":1,"Steps":"Annote gap reactions","Group":"Reconstruction Output"}