QuickView Scores

Quick overview of the ###ModelName reconstruction scores, as generated with the 'generateMetaboReport.m' in the COBRA Toolbox.

###OverallScore %

Overall
Score

###ScoreConsistency %

Consistency
Score

###ScoreAnnotationMetabolites %

Metabolite
Score

###ScoreAnnotationReactions %

Reaction
Score

###ScoreAnnotationGenes %

Gene
Score

###ScoreAnnotationSBO %

SBO Term Score

Reconstruction details

Total Metabolites: ###NumMets

List of all metabolites in ###ModelName:
  • ###ListNumMets

Total Reactions: ###NumRxns

List of all metabolites in ###ModelName:
  • ###ListNumRxns

Total Genes: ###NumGenes

Total Compartments: ###NumComp

Metabolic Coverage: ###MetCov

Unique Metabolites: ###NumMUnique

Unique Metabolites in ###ModelName:
  • ###ListMetUnique

Metabolites without Charge: ###NumMetNoCharge

Metabolites without charge in ###ModelName
  • ###ListNumMetNoCharge

Metabolites without Formula: ###NumMetNoForm

Metabolites without formulae in ###ModelName
  • ###ListNumMetNoForm

Medium Components: ###MedComp

Medium Compoments in ###ModelName
  • ###ListMedComp

Metabolic Reactions: ###NumMetRxns

Metabolic transformation reactions in ###ModelName:
  • ###ListNumMetRxns

Transport Reactions: ###NumTransRxns

Transport reactions in ###ModelName:
  • ###ListNumTransRxns

Exchange Reactions: ###NumExRxns

Exchange reactions in ###ModelName:
  • ###ListNumExRxns

Demand Reactions: ###NumDmRxns

Demand reactions in ###ModelName:
  • ###ListNumDmRxns

Sink Reactions: ###NumSinkRxns

Sink reactions in ###ModelName:
  • ###ListNumSinkRxns

Biomass Reaction(s): ###NumBmRxns

Biomass reaction(s) in ###ModelName:
  • ###ListNumBmRxns

Reactions without GPRs: ###NumRxnWoGpr %

Reactions without GPRs in ###ModelName:
  • ###ListNumRxnWoGpr

Transport reactions without GPRs: ###NumTRxnWoGpr %

Transport reactions without GPRs in ###ModelName:
  • ###ListNumTRxnWoGpr

Universally blocked reactions: ###NumBlockedR %

Universally blocked reactions in ###ModelName:
  • ###ListNumBlockedR

Deadend metabolites: ###NumDeadM %

Deadend metabolites in ###ModelName:
  • ###ListNumDeadM

Reaction in stoichiometrically balanced cycles: ###NumStoichCycleRxns %

Reaction in stoichiometrically balanced cycles in ###ModelName:
  • ###ListNumStoichCycleRxns

Ratio Min/Max Non-Zero Coefficients: ###NumMinMaxCoeff

Ratio Min/Max Non-Zero Coefficients in ###ModelName:
  • ###ListNumMinMaxCoeff

Rank of the stoichiometric matrix: ###NumRank

Scored annotation properties

Stoichiometric Consistency: ###NumConsRxns %

Stoichiometrically inconsistent reactions in ###ModelName:
  • ###ListNumConsRxns

Mass balanced reactions: ###NumBalRxns %

Mass unbalanced reactions in ###ModelName:
  • ###ListNumBalRxns

Charge balanced reactions: ###NumChargeRxns %

Charge unbalanced reactions in ###ModelName:
  • ###ListNumChargeRxns

Metabolite Connectivity: ###NumMetConnec %

Metabolites that do not appear in any reaction in ###ModelName:
  • ###ListNumMetConnec

Unbounded flux in unconstraint medium: ###NumUnboundR %

Metabolites that do not appear in any reaction in ###ModelName:
  • ###ListNumUnboundR

Score sub total: ###ScoreConsistency %

Presence of Metabolite Annotation: ###NumMAnnoAny %

Metabolites that have no annotation in ###ModelName:
  • ###ListNumMAnnoAny

Metabolite Annotation per database:

Pubchem compound ID: ###NumMetPubCh %

Metabolites without Pubchem ID in ###ModelName
  • ###ListNumMetPubCh

Kegg compound ID: ###NumMetKegg %

Metabolites without Kegg ID in ###ModelName
  • ###ListNumMetKegg

SEED compound ID: ###NumMetSeed %

Metabolites without SEED ID in ###ModelName
  • ###ListNumMetSeed

Inchi key: ###NumMetIKey %

Metabolites without inchi key in ###ModelName
  • ###ListNumMetIKey

Inchi string: ###NumMetIString %

Metabolites without inchi string in ###ModelName
  • ###ListNumMetIString

CheBi ID: ###NumMetChebi %

Metabolites without CheBi ID in ###ModelName
  • ###ListNumMetChebi

HMDB ID: ###NumMetHmdb %

Metabolites without HMDB ID in ###ModelName
  • ###ListNumMetHmdb

Reactome ID: ###NumMetReac %

Metabolites without conform Reactome ID in ###ModelName
  • ###ListNumMetReac

MetaNetX Chemical ID: ###NumMetMetNetX %

Metabolites without MetaNetX Chemical ID in ###ModelName
  • ###ListNumMetMetNetX

BiGG Metabolite ID: ###NumMetBigg %

Metabolites without BiGG Metabolite ID in ###ModelName
  • ###ListNumMetBigg

BioCyc ID: ###NumMetBioc %

Metabolites without BioCyc Metabolite ID in ###ModelName
  • ###ListNumMetBioc

Metabolite Annotation Conformity per database:

Pubchem compound ID: ###NumMetCPubCh %

Metabolites without conform Pubchem ID in ###ModelName
  • ###ListNumMetCPubCh

Kegg compound ID: ###NumMetCKegg %

Metabolites without conform Kegg ID in ###ModelName
  • ###ListNumMetCKegg

SEED compound ID: ###NumMetCSeed %

Metabolites without conform SEED ID in ###ModelName
  • ###ListNumMetCSeed

Inchi key: ###NumMetCIKey %

Metabolites without conform inchi key in ###ModelName
  • ###ListNumMetCIKey

Inchi string: ###NumMetCIString %

Metabolites without conform inchi string in ###ModelName
  • ###ListNumMetCIString

CheBi ID: ###NumMetCChebi %

Metabolites without conform CheBi ID in ###ModelName
  • ###ListNumMetCChebi

HMDB ID: ###NumMetCHmdb %

Metabolites without conform HMDB ID in ###ModelName
  • ###ListNumMetCHmdb

Reactome ID: ###NumMetCReac %

Metabolites without conform Reactome ID in ###ModelName
  • ###ListNumMetCReac

MetaNetX Chemical ID: ###NumMetCMetNetX %

Metabolites without conform MetaNetX Chemical ID in ###ModelName
  • ###ListNumMetCMetNetX

BiGG Metabolite ID: ###NumMetCBigg %

Metabolites without conform BiGG Metabolite ID in ###ModelName
  • ###ListNumMetCBigg

BioCyc ID: ###NumMetCBioc %

Metabolites without conform BioCyc Metabolite ID in ###ModelName
  • ###ListNumMetCBioc

Score sub total: ###ScoreAnnotationMetabolites %

Presence of Reaction Annotation: ###NumRAnnoAny %

Reactions without any annotation in ###ModelName:
  • ###ListNumRAnnoAny

Reaction Annotation per database:

Rhea ID: ###NumRRhea %

Reactions without Rhea ID in ###ModelName
  • ###ListNumRRhea

Kegg Reaction ID: ###NumRKegg %

Reactions without Kegg ID in ###ModelName
  • ###ListNumRKegg

SEED Reaction ID: ###NumRSeed %

Reactions without SEED ID in ###ModelName
  • ###ListNumRSeed

MetaNetX Reaction ID: ###NumRMetX %

Reactions without MetaNetX ID in ###ModelName
  • ###ListNumRMetX

BiGG Reaction ID: ###NumRBigg %

Reactions without BiGG ID in ###ModelName
  • ###ListNumRBigg

Reactome Reaction ID: ###NumRReac %

Reactions without Reactome ID in ###ModelName
  • ###ListNumRReac

BRENDA ID: ###NumRBren %

Reactions without BRENDA ID in ###ModelName
  • ###ListNumRBren

BioCyc Reaction ID: ###NumRBioc %

Reactions without BioCyc Reaction ID in ###ModelName
  • ###ListNumRBioc

EC number: ###NumREcn %

Reactions without EC number in ###ModelName
  • ###ListNumREcn

Reaction Annotation Conformity per database:

Rhea ID: ###NumCRRhea %

Reactions with non-conform Rhea ID in ###ModelName
  • ###ListNumCRRhea

Kegg Reaction ID: ###NumCRKegg %

Reactions with non-conform Kegg ID in ###ModelName
  • ###ListNumCRKegg

SEED Reaction ID: ###NumCRSeed %

Reactions with non-conform SEED ID in ###ModelName
  • ###ListNumCRSeed

MetaNetX Reaction ID: ###NumCRMetX %

Reactions with non-conform MetaNetX ID in ###ModelName
  • ###ListNumCRMetX

BiGG Reaction ID: ###NumCRBigg %

Reactions with non-conform BiGG ID in ###ModelName
  • ###ListNumCRBigg

Reactome Reaction ID: ###NumCRReac %

Reactions with non-conform Reactome ID in ###ModelName
  • ###ListNumCRReac

BRENDA ID: ###NumCRBren %

Reactions with non-conform BRENDA ID in ###ModelName
  • ###ListNumCRBren

BioCyc Reaction ID: ###NumCRBioc %

Reactions with non-conform BioCyc Reaction ID in ###ModelName
  • ###ListNumCRBioc

EC number: ###NumCREcn %

Reactions with non-conform EC number in ###ModelName
  • ###ListNumCREcn

Score sub total: ###ScoreAnnotationReactions %

Presence of Gene Annotation: ###NumGAnnoAny %

Genes without any annotation in ###ModelName:
  • ###ListNumGAnnoAny

Gene Annotation per database:

RefSeq ID: ###NumGRefSeq %

Genes without RefSeq ID in ###ModelName
  • ###ListNumGRefSeq

UniProt ID: ###NumGUniProt %

Genes without UniProt ID in ###ModelName
  • ###ListNumGUniProt

EcoGene ID: ###NumGEcoGene %

Genes without EcoGene ID in ###ModelName
  • ###ListNumGEcoGene

KEGG Gene ID: ###NumGKegg %

Genes without Kegg ID in ###ModelName
  • ###ListNumGKegg

NCBI Gene ID: ###NumGNCBIG %

Genes without NCBI Gene ID in ###ModelName
  • ###ListNumGNCBIG

NCBI Protein ID: ###NumGNCBIP %

Genes without NCBI Protein ID in ###ModelName
  • ###ListNumGNCBIP

CCDS ID: ###NumGCCDS %

Genes without CCDS ID in ###ModelName
  • ###ListNumGCCDS

HPRD ID: ###NumGHPRD %

Genes without HPRD ID in ###ModelName
  • ###ListNumGHPRD

ASAP ID: ###NumGASAP %

Genes without ASAP ID in ###ModelName
  • ###ListNumGASAP

Gene Annotation Conformity per database:

RefSeq ID: ###NumCGRefSeq %

Genes without conform RefSeq ID in ###ModelName
  • ###ListNumCGRefSeq

UniProt ID: ###NumCGUniProt %

Genes without conform UniProt ID in ###ModelName
  • ###ListNumCGUniProt

EcoGene ID: ###NumCGEcoGene %

Genes without conform EcoGene ID in ###ModelName
  • ###ListNumCGEcoGene

KEGG Gene ID: ###NumCGKegg %

Genes without conform Kegg ID in ###ModelName
  • ###ListNumCGKegg

NCBI Gene ID: ###NumCGNCBIG %

Genes without conform NCBI Gene ID in ###ModelName
  • ###ListNumCGNCBIG

NCBI Protein ID: ###NumCGNCBIP %

Genes without conform NCBI Protein ID in ###ModelName
  • ###ListNumCGNCBIP

CCDS ID: ###NumCGCCDS %

Genes without conform CCDS ID in ###ModelName
  • ###ListNumCGCCDS

HPRD ID: ###NumCGHPRD %

Genes without conform HPRD ID in ###ModelName
  • ###ListNumCGHPRD

ASAP ID: ###NumCGASAP %

Genes without conform ASAP ID in ###ModelName
  • ###ListNumCGASAP

Score sub total: ###ScoreAnnotationGenes %

Metabolite General SBO Terms: ###NumMSBOAny %

Metabolites without any SBO Term in ###ModelName:
  • ###ListNumMSBOAny

Metabolite SBO:0000247 Presence: ###NumMetSBO247 %

Reaction General SBO Terms: ###NumRSBOAny %

Reactions without any SBO Term in ###ModelName
  • ###ListNumRSBOAny

Metabolic reaction SBO:0000176 Presence: ###NumRSBO176 %

Transport reaction SBO:0000185 Presence: ###NumRSBO185 %

Exchange reaction SBO:0000627 Presence: ###NumRSBO627 %

Demand reaction SBO:0000628 Presence: ###NumRSBO628 %

Sink reaction SBO:0000632 Presence: ###NumRSBO632 %

Biomass reaction SBO:0000629 Presence: ###NumRSBO629 %

Gene General SBO Terms: ###NumGSBOAny %

Genes without any SBO Term in ###ModelName
  • ###ListNumGSBOAny

GeneSBO:0000243 Presence: ###NumGSBO243 %

Score sub total: ###ScoreAnnotationSBO %