KarrLab/obj_tables

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examples/sbtab/SBtab.tsv

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!!ObjTables type='Schema' tableFormat='row' name='SBtab' description='Table/model and column/attribute definitions' date='2019-9-13' objTablesVersion='0.0.8'                
!Name    !Type    !Parent    !Format    !Description
Comment    Attribute    Reaction    String    Comment
ReferenceName    Attribute    Reaction    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Reaction    String    Reference PubMed ID
ReferenceDOI    Attribute    Reaction    String    Reference DOI
Description    Attribute    Reaction    String    Description of the row element
Modifier    Attribute    Reaction    String    Modifier of this reaction
Name    Attribute    Reaction    String    Entity name
MiriamAnnotations    Attribute    Reaction    String    Entity ID
Type    Attribute    Reaction    String    Biochemical type of entity
Symbol    Attribute    Reaction    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Reaction    Float    x coordinate for graphical display
PositionY    Attribute    Reaction    Float    y coordinate for graphical display
ID    Attribute    Reaction    String    Reaction shortname
SBML:reaction:id    Attribute    Reaction    String    SBML ID of reaction
ReactionFormula    Attribute    Reaction    LongString    Reaction formula
Location    Attribute    Reaction    String    Compartment for localised reaction
Enzyme    Attribute    Reaction    String    Enzyme catalysing the reaction
Model    Attribute    Reaction    String    Model(s) in which the reaction is involved
Pathway    Attribute    Reaction    String    Pathway(s) in which the reaction is involved
SubreactionOf    Attribute    Reaction    String    Mark as subreaction of a (lumped) reaction
IsComplete    Attribute    Reaction    Boolean    Reaction formula includes all cofactors etc.
IsReversible    Attribute    Reaction    Boolean    Reaction should be treated as irreversible
IsInEquilibrium    Attribute    Reaction    Boolean    Reaction approximately in equilibrium
IsExchangeReaction    Attribute    Reaction    Boolean    Some reactants are left out
Flux    Attribute    Reaction    Float    Metabolic flux through the reaction
IsNonEnzymatic    Attribute    Reaction    Boolean    Non-catalysed reaction
KineticLaw    Attribute    Reaction    LongString    Kinetic law of the reaction
KineticLaw:Name    Attribute    Reaction    String    Name of the kinetic law
KineticLaw:Formula    Attribute    Reaction    String    Rate law formula
Gene    Attribute    Reaction    String    Name of the gene for the catalysing enzyme
Gene:Symbol    Attribute    Reaction    String    Name of the gene for the catalysing enzyme
Operon    Attribute    Reaction    String    Operon for the gene of the catalysing enzyme
Enzyme:SBML:species:id    Attribute    Reaction    String    SBML ID of enzyme
Enzyme:SBML:parameter:id    Attribute    Reaction    String    SBML ID of enzyme
BuildReaction    Attribute    Reaction    Boolean    Include reaction in SBML model
BuildEnzyme    Attribute    Reaction    Boolean    Include enzyme in SBML model
BuildEnzymeProduction    Attribute    Reaction    Boolean    Describe enzyme production in SBML model
SBOTerm    Attribute    Reaction    String    SBO term of the entity
Identifiers    Attribute    Reaction    String    Annotation of the entity
Identifiers:kegg.reaction    Attribute    Reaction    String    Annotation of the entity
Identifiers:obo.sbo    Attribute    Reaction    String    Annotation of the entity
Identifiers:ec-code    Attribute    Reaction    String    Annotation of the entity
SBML:fbc:GeneAssociation    Attribute    Reaction    LongString    Gene Association from the FBC package
SBML:fbc:LowerBound    Attribute    Reaction    String    Reactions Lower Bound of the FBC package
SBML:fbc:UpperBound    Attribute    Reaction    String    Reactions Upper Bound of the FBC package
Regulator    Attribute    Reaction    String    
NameForPlots    Attribute    Reaction    String    
Comment    Attribute    Compound    String    Comment
ReferenceName    Attribute    Compound    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Compound    String    Reference PubMed ID
ReferenceDOI    Attribute    Compound    String    Reference DOI
Description    Attribute    Compound    String    Description of the row element
Name    Attribute    Compound    String    Entity name
MiriamAnnotations    Attribute    Compound    String    Entity ID
Type    Attribute    Compound    String    Biochemical type of entity
Symbol    Attribute    Compound    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Compound    Float    x coordinate for graphical display
PositionY    Attribute    Compound    Float    y coordinate for graphical display
ID    Attribute    Compound    String    Compound shortname
SBML:species:id    Attribute    Compound    String    SBML species ID of the entity
SBML:speciestype:id    Attribute    Compound    String    SBML speciestype ID of the entity
InitialValue    Attribute    Compound    Float    Initial amount or concentration
InitialConcentration    Attribute    Compound    Float    Initial amount or concentration
Unit    Attribute    Compound    String    Unit for initial value
Location    Attribute    Compound    String    Compartment for localised entities
State    Attribute    Compound    String    State of the entity
CompoundSumFormula    Attribute    Compound    String    Chemical sum formula
StructureFormula    Attribute    Compound    String    Chemical structure formula
Charge    Attribute    Compound    Integer    Electrical charge number
Mass    Attribute    Compound    Float    Molecular mass
IsConstant    Attribute    Compound    Boolean    Substance with fixed concentrations
EnzymeRole    Attribute    Compound    String    Enzymatic activity
RegulatorRole    Attribute    Compound    String    Regulatory activity
SBOTerm    Attribute    Compound    String    SBO term of the entity
Identifiers    Attribute    Compound    String    Annotation of the entity
Identifiers:sbo.kegg    Attribute    Compound    String    Annotation of the entity
Identifiers:kegg.compound    Attribute    Compound    String    Annotation of the entity
Identifiers:obo.chebi    Attribute    Compound    String    Annotation of the entity
SBML:fbc:ChemicalFormula    Attribute    Compound    String    Compounds chemical formula for the FBC package
SBML:fbc:Charge    Attribute    Compound    Float    Compounds charge for the FBC package
HasOnlySubstanceUnits    Attribute    Compound    Boolean    
NameForPlots    Attribute    Compound    String    
Comment    Attribute    Enzyme    String    Comment
ReferenceName    Attribute    Enzyme    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Enzyme    String    Reference PubMed ID
ReferenceDOI    Attribute    Enzyme    String    Reference DOI
Description    Attribute    Enzyme    String    Description of the row element
Name    Attribute    Enzyme    String    Entity name
MiriamAnnotations    Attribute    Enzyme    String    Entity ID
Type    Attribute    Enzyme    String    Biochemical type of entity
Symbol    Attribute    Enzyme    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Enzyme    Float    x coordinate for graphical display
PositionY    Attribute    Enzyme    Float    y coordinate for graphical display
ID    Attribute    Enzyme    String    Enzyme shortname
CatalysedReaction    Attribute    Enzyme    String    Catalysed reaction
KineticLaw    Attribute    Enzyme    String    Catalysed reaction
KineticLaw:Name    Attribute    Enzyme    String    Name of the kinetic law
KineticLaw:Formula    Attribute    Enzyme    String    Rate law formula
Pathway    Attribute    Enzyme    String    Pathway name (free text)
Gene    Attribute    Enzyme    String    Gene coding for enzyme (shortname)
Identifiers    Attribute    Enzyme    String    Annotation of the entity
Comment    Attribute    Protein    String    Comment
ReferenceName    Attribute    Protein    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Protein    String    Reference PubMed ID
ReferenceDOI    Attribute    Protein    String    Reference DOI
Description    Attribute    Protein    String    Description of the row element
Name    Attribute    Protein    String    Entity name
MiriamAnnotations    Attribute    Protein    String    Entity ID
Type    Attribute    Protein    String    Biochemical type of entity
Symbol    Attribute    Protein    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Protein    Float    x coordinate for graphical display
PositionY    Attribute    Protein    Float    y coordinate for graphical display
ID    Attribute    Protein    String    Protein shortname
Gene    Attribute    Protein    String    Gene shortname
Mass    Attribute    Protein    Float    Protein mass
Size    Attribute    Protein    Float    Protein size
Comment    Attribute    Compartment    String    Comment
ReferenceName    Attribute    Compartment    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Compartment    String    Reference PubMed ID
ReferenceDOI    Attribute    Compartment    String    Reference DOI
Description    Attribute    Compartment    String    Description of the row element
Name    Attribute    Compartment    String    Entity name
MiriamAnnotations    Attribute    Compartment    String    Entity ID
Type    Attribute    Compartment    String    Biochemical type of entity
Symbol    Attribute    Compartment    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Compartment    Float    x coordinate for graphical display
PositionY    Attribute    Compartment    Float    y coordinate for graphical display
ID    Attribute    Compartment    String    Compartment shortname
SBML:compartment:id    Attribute    Compartment    String    SBML compartment ID
OuterCompartment    Attribute    Compartment    String    Surrounding compartment (short)
OuterCompartment:SBML:compartment:id    Attribute    Compartment    String    Surrounding compartment (name)
Size    Attribute    Compartment    Float    Compartment size
Unit    Attribute    Compartment    String    Physical unit
SBOTerm    Attribute    Compartment    String    SBO term of the entity
Identifiers    Attribute    Compartment    String    Annotation of the entity
Identifiers:sbo.go    Attribute    Compartment    String    Annotation of the entity
Comment    Attribute    Quantity    String    Comment
ReferenceName    Attribute    Quantity    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Quantity    String    Reference PubMed ID
ReferenceDOI    Attribute    Quantity    String    Reference DOI
Description    Attribute    Quantity    String    Description of the row element
Name    Attribute    Quantity    String    Entity name
MiriamAnnotations    Attribute    Quantity    String    Entity ID
Type    Attribute    Quantity    String    Biochemical type of entity
Symbol    Attribute    Quantity    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Quantity    Float    x coordinate for graphical display
PositionY    Attribute    Quantity    Float    y coordinate for graphical display
ID    Attribute    Quantity    String    Quantity shortname
Quantity    Attribute    Quantity    String    Quantity name
Reference    Attribute    Quantity    String    Reference name
QuantityName    Attribute    Quantity    String    Quantity (name)
QuantityType    Attribute    Quantity    String    Quantity type (e.g. from SBO)
Value    Attribute    Quantity    Float    Simple value
Mean    Attribute    Quantity    Float    Algebraic mean
Std    Attribute    Quantity    Float    Standard deviation (positive)
Min    Attribute    Quantity    Float    Lower bound
Max    Attribute    Quantity    Float    Upper bound
Median    Attribute    Quantity    Float    Median
GeometricMean    Attribute    Quantity    Float    Geometric mean
Sign    Attribute    Quantity    Enum(['+', '-', '0'], default='0')    Sign
ProbDist    Attribute    Quantity    String    Probability distribution
SBML:parameter:id    Attribute    Quantity    String    Parameter ID in SBML file
Unit    Attribute    Quantity    String    Physical unit
Scale    Attribute    Quantity    String    Scale (e.g. logarithm)
Time    Attribute    Quantity    Float    Time value
TimePoint    Attribute    Quantity    String    Time point name or identifier
Condition    Attribute    Quantity    String    experimental condition name (free text)
pH    Attribute    Quantity    Float    pH value in measurement
Temperature    Attribute    Quantity    Float    Temperature in measurement
Location    Attribute    Quantity    String    Compartment (shortname)
Location:SBML:compartment:id    Attribute    Quantity    String    SBML ID of compartment
Compound    Attribute    Quantity    String    Related compound (shortname)
Compound:SBML:species:id    Attribute    Quantity    String    SBML ID of compound
Reaction    Attribute    Quantity    String    Related reaction (shortname)
Reaction:SBML:reaction:id    Attribute    Quantity    String    SBML ID of reaction
Enyzme    Attribute    Quantity    String    Related enzyme (shortname)
Enyzme:SBML:species:id    Attribute    Quantity    String    SBML ID of enzyme
Enyzme:SBML:parameter:id    Attribute    Quantity    String    SBML ID of enzyme
Gene    Attribute    Quantity    String    Related gene
Organism    Attribute    Quantity    String    Organism
Provenance    Attribute    Quantity    String    Provenance of the entity
SBOTerm    Attribute    Quantity    String    SBO term of the entity
Identifiers    Attribute    Quantity    String    Annotation of the entity
Identifiers:kegg.reaction    Attribute    Quantity    String    Annotation of the entity
Identifiers:kegg.compound    Attribute    Quantity    String    Annotation of the entity
Identifiers:obo.chebi    Attribute    Quantity    String    Annotation of the entity
Reaction:Identifiers:kegg.reaction    Attribute    Quantity    String    Annotation of the entity
Compound:Identifiers:kegg.compound    Attribute    Quantity    String    Annotation of the entity
BiologicalElement    Attribute    Quantity    String    Biological element
MathematicalType    Attribute    Quantity    String    Mathematical type
DataGeometricStd    Attribute    Quantity    Float    Data geometric standard error
PriorMedian    Attribute    Quantity    Float    Prior Median
PriorStd    Attribute    Quantity    Float    Prior Std
PriorGeometricStd    Attribute    Quantity    Float    Prior Geometric Std
LowerBound    Attribute    Quantity    Float    Lower bound
UpperBound    Attribute    Quantity    Float    Lower bound
DataStd    Attribute    Quantity    Float    Data Standard Error
PhysicalType    Attribute    Quantity    String    Physical Type
Dependence    Attribute    Quantity    String    Dependence
UseAsPriorInformation    Attribute    Quantity    Boolean    Use as prior information
SBMLElement    Attribute    Quantity    String    SBML element
Abbreviation    Attribute    Quantity    String    Abbreviation
MatrixInfo    Attribute    Quantity    String    Matrix build up information
SBO:equilibrium_constant    Attribute    Quantity    Float    
SBO:Identifiers:obo.sbo    Attribute    Quantity    String    
SBO:concentration    Attribute    Quantity    Float    
SBO:concentration [mM:Log10]:Median    Attribute    Quantity    Float    
ValueType    Attribute    Quantity    String    
Concentration:Min    Attribute    Quantity    Float    
Concentration:Max    Attribute    Quantity    Float    
Parameter:SBML:parameter:id    Attribute    Quantity    String    
Comment    Attribute    Regulator    String    Comment
ReferenceName    Attribute    Regulator    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Regulator    String    Reference PubMed ID
ReferenceDOI    Attribute    Regulator    String    Reference DOI
Description    Attribute    Regulator    String    Description of the row element
Name    Attribute    Regulator    String    Entity name
MiriamAnnotations    Attribute    Regulator    String    Entity ID
Type    Attribute    Regulator    String    Biochemical type of entity
Symbol    Attribute    Regulator    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Regulator    Float    x coordinate for graphical display
PositionY    Attribute    Regulator    Float    y coordinate for graphical display
ID    Attribute    Regulator    String    Regulator shortname
State    Attribute    Regulator    String    State of the regulator
TargetGene    Attribute    Regulator    String    Target gene
TargetOperon    Attribute    Regulator    String    Target operon
TargetPromoter    Attribute    Regulator    String    Target promoter
Identifiers    Attribute    Regulator    String    Annotation of the entity
Comment    Attribute    Gene    String    Comment
ReferenceName    Attribute    Gene    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Gene    String    Reference PubMed ID
ReferenceDOI    Attribute    Gene    String    Reference DOI
Description    Attribute    Gene    String    Description of the row element
Name    Attribute    Gene    String    Entity name
MiriamAnnotations    Attribute    Gene    String    Entity ID
Type    Attribute    Gene    String    Biochemical type of entity
Symbol    Attribute    Gene    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    Gene    Float    x coordinate for graphical display
PositionY    Attribute    Gene    Float    y coordinate for graphical display
ID    Attribute    Gene    String    Gene shortname
LocusName    Attribute    Gene    String    Gene locus name
GeneProduct    Attribute    Gene    String    Gene product shortname
GeneProduct:SBML:species:id    Attribute    Gene    String    SBML ID of protein
Operon    Attribute    Gene    String    Operon in which gene is located
Identifiers    Attribute    Gene    String    Annotation of the entity
SBML:fbc:ID    Attribute    Gene    String    Unique identifier of the gene in the FBC package
SBML:fbc:Name    Attribute    Gene    String    Name of the gene in the FBC package
SBML:fbc:GeneProduct    Attribute    Gene    Boolean    Flag indicating if the gene is an FBC gene product
SBML:fbc:GeneAssociation    Attribute    Gene    Boolean    Flag indicating if the gene is an FBC gene association
SBML:fbc:Label    Attribute    Gene    String    Label of the gene in the FBC package
Comment    Attribute    Relation    String    Comment
ReferenceName    Attribute    Relation    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    Relation    String    Reference PubMed ID
ReferenceDOI    Attribute    Relation    String    Reference DOI
Description    Attribute    Relation    String    Description of the row element
ID    Attribute    Relation    String    Type of quantitative relation
FromObject    Attribute    Relation    String    Element at beginning of arrow
ToObject    Attribute    Relation    String    Element at arrowhead
IsSymmetric    Attribute    Relation    Boolean    Flag indicating non-symmetric relations
Value:QuantityType    Attribute    Relation    Float    Numerical value assigned to the relation
ComponentName    Attribute    Definition    String    Name of component (table, column, attribute to be defined)
ComponentType    Attribute    Definition    String    Type of component
IsPartOf    Attribute    Definition    String    Name of parent component
Format    Attribute    Definition    String    Format
Description    Attribute    Definition    String    Free text description of component
Comment    Attribute    QuantityMatrix    String    Comment
ReferenceName    Attribute    QuantityMatrix    String    Reference title, authors, etc. (as free text)
ReferencePubMed    Attribute    QuantityMatrix    String    Reference PubMed ID
ReferenceDOI    Attribute    QuantityMatrix    String    Reference DOI
Description    Attribute    QuantityMatrix    String    Description of the row element
Name    Attribute    QuantityMatrix    String    Entity name
MiriamAnnotations    Attribute    QuantityMatrix    String    Entity ID
Type    Attribute    QuantityMatrix    String    Biochemical type of entity
Symbol    Attribute    QuantityMatrix    String    Short symbol (e.g. gene symbol)
PositionX    Attribute    QuantityMatrix    Float    x coordinate for graphical display
PositionY    Attribute    QuantityMatrix    Float    y coordinate for graphical display
Time    Attribute    QuantityMatrix    Float    Time value
TimePoint    Attribute    QuantityMatrix    String    Time point name or identifier
>Table:Column    Attribute    QuantityMatrix    String    Pointer to column in another table
>Document:Table:Column    Attribute    QuantityMatrix    String    Pointer to column in another document
ID    Attribute    QuantityMatrix    String    Quantity shortname
QuantityName    Attribute    QuantityMatrix    String    Quantity (name)
QuantityType    Attribute    QuantityMatrix    String    Quantity type (e.g. from SBO)
Value    Attribute    QuantityMatrix    Float    Simple value
Mean    Attribute    QuantityMatrix    Float    Algebraic mean
Std    Attribute    QuantityMatrix    Float    Standard deviation (positive)
Min    Attribute    QuantityMatrix    Float    Lower bound
Max    Attribute    QuantityMatrix    Float    Upper bound
Median    Attribute    QuantityMatrix    Float    Median
GeometricMean    Attribute    QuantityMatrix    Float    Geometric mean
Sign    Attribute    QuantityMatrix    Enum(['+', '-', '0'], default='0')    Sign
ProbDist    Attribute    QuantityMatrix    String    Probability distribution
SBML:parameter:id    Attribute    QuantityMatrix    String    Parameter ID in SBML file
Unit    Attribute    QuantityMatrix    String    Physical unit
Scale    Attribute    QuantityMatrix    String    Scale (e.g. logarithm)
Compound    Attribute    QuantityMatrix    String    Related compound (shortname)
Compound:SBML:species:id    Attribute    QuantityMatrix    String    SBML ID of compound
Reaction    Attribute    QuantityMatrix    String    Related reaction (shortname)
Reaction:SBML:reaction:id    Attribute    QuantityMatrix    String    SBML ID of reaction
Enyzme    Attribute    QuantityMatrix    String    Related enzyme (shortname)
Enyzme:SBML:species:id    Attribute    QuantityMatrix    String    SBML ID of enzyme
Enyzme:SBML:parameter:id    Attribute    QuantityMatrix    String    SBML ID of enzyme
Protein    Attribute    QuantityMatrix    String    Related enzyme (shortname)
Protein:SBML:species:id    Attribute    QuantityMatrix    String    SBML ID of enzyme
Gene    Attribute    QuantityMatrix    String    Related gene
Identifiers:obo.chebi    Attribute    QuantityMatrix    String    
>Concentration:Glucose    Attribute    QuantityMatrix    Float    
>Concentration:Fructose    Attribute    QuantityMatrix    Float    
>Sample:t0    Attribute    QuantityMatrix    Float    
>Sample:t1    Attribute    QuantityMatrix    Float    
>TP:t0:mean    Attribute    QuantityMatrix    Float    
>TP:t0:std    Attribute    QuantityMatrix    Float    
>TP:t1:mean    Attribute    QuantityMatrix    Float    
>TP:t1:std    Attribute    QuantityMatrix    Float    
ReactionID    Attribute    StoichiometricMatrix    String    Reaction shortname
Stoichiometry    Attribute    StoichiometricMatrix    String    Stoichiometric coefficient of the reactant
Substrate    Attribute    StoichiometricMatrix    String    Substrate of the reaction
Product    Attribute    StoichiometricMatrix    String    Product of the reaction
Location    Attribute    StoichiometricMatrix    String    Compartment for localised reaction
Sample    Attribute    Measurement    String    Measurement value shortname
Time    Attribute    Measurement    String    Time at which measurement was taken
Unit    Attribute    Measurement    String    Measurement unit
ValueType    Attribute    Measurement    String    Type of value (mean, standard deviation, etc)
Description    Attribute    Measurement    String    Description of data value
QuantityType    Attribute    QuantityInfo    String    QuantityType (e.g. from SBO)
Symbol    Attribute    QuantityInfo    String    Symbol for the quantity type
Unit    Attribute    QuantityInfo    String    Unit for the Median value
Constant    Attribute    QuantityInfo    String    Is this value constant
Element    Attribute    QuantityInfo    String    A related element
RelatedElement    Attribute    QuantityInfo    String    A related element
Scaling    Attribute    QuantityInfo    String    A scaling factor
Dependence    Attribute    QuantityInfo    String    Is this value dependent on something
PriorMedian    Attribute    QuantityInfo    Float    Prior median value
PriorStd    Attribute    QuantityInfo    Float    Prior median standard deviation
LowerBound    Attribute    QuantityInfo    Float    Lower bound for this quantity type
UpperBound    Attribute    QuantityInfo    Float    Upper bound for this quantity type
ErrorStd    Attribute    QuantityInfo    Float    Error of standard deviation
DataStd    Attribute    QuantityInfo    Float    Error of standard deviation
SBMLElement    Attribute    QuantityInfo    String    Corresponding SBML element
SBMLElementType    Attribute    QuantityInfo    String    Corresponding SBML element
Abbreviation    Attribute    QuantityInfo    String    Abbreviation of quantity type
ID    Attribute    QuantityInfo    String    Abbreviation of quantity type
MatrixInfo    Attribute    QuantityInfo    String    Information on the matrix production
Option    Attribute    PbConfig    String    Which option is addressed
Value    Attribute    PbConfig    String    What value is the option set to
UID:Contingency    Attribute    rxnconContingencyList    Integer    ID for contingency
Target    Attribute    rxnconContingencyList    String    Contingency target
Contingency    Attribute    rxnconContingencyList    String    Contingency type
Modifier    Attribute    rxnconContingencyList    String    Target modifier
Reference:Identifiers:pubmed    Attribute    rxnconContingencyList    String    Pubmed ID
Quality    Attribute    rxnconContingencyList    String    Contingency quality
Comment    Attribute    rxnconContingencyList    String    Comment
InternalComplexID    Attribute    rxnconContingencyList    String    Internal ID for processing
ID    Attribute    rxnconReactionList    Integer    ID for reaction
UID:Reaction    Attribute    rxnconReactionList    String    Reaction string
ComponentA:Name    Attribute    rxnconReactionList    String    Name for Component A
ComponentA:Domain    Attribute    rxnconReactionList    String    Domain of Component A
ComponentA:Residue    Attribute    rxnconReactionList    String    Residue of Component A
Reaction    Attribute    rxnconReactionList    String    Reaction type
ComponentB:Name    Attribute    rxnconReactionList    String    Name for Component B
ComponentB:Domain    Attribute    rxnconReactionList    String    Domain of Component B
ComponentB:Residue    Attribute    rxnconReactionList    String    Residue of Component B
Quality    Attribute    rxnconReactionList    String    Quality of reaction
Literature:Identifiers:pubmed    Attribute    rxnconReactionList    String    Pubmed ID
Comment    Attribute    rxnconReactionList    String    Comment
ID    Attribute    FbcObjective    String    Unique identifier of objective in FBC package
Name    Attribute    FbcObjective    String    Name of objective in FBC package
SBML:fbc:type    Attribute    FbcObjective    String    Type of objective in FBC package
SBML:fbc:active    Attribute    FbcObjective    Boolean    Flag indicating if the objective is active
SBML:fbc:objective    Attribute    FbcObjective    String    FBC objective as sum of coefficients times reaction IDs
SBML:fbc:reaction    Attribute    FbcObjective    String    
ID    Attribute    Layout    String    Unique identifier of layout package
Name    Attribute    Layout    String    Name of layout in plugin
SBML:layout:modelEntity    Attribute    Layout    String    Declares the SBML model entity
SBML:layout:compartment:id    Attribute    Layout    String    SBML identifier of the compartment
SBML:layout:reaction:id    Attribute    Layout    String    SBML identifier of the reaction
SBML:layout:species:id    Attribute    Layout    String    SBML identifier of the species
SBML:layout:curveSegment    Attribute    Layout    String    Type of curve segment (Start, End, BasePoints)
SBML:layout:X    Attribute    Layout    Float    Coordinate on X axis
SBML:layout:Y    Attribute    Layout    Float    Coordinate on Y axis
SBML:layout:width    Attribute    Layout    Float    Width of the element
SBML:layout:height    Attribute    Layout    Float    Height of the element
SBML:layout:text    Attribute    Layout    String    Text label of the element
SBML:layout:speciesRole    Attribute    Layout    String    Role of the species in the reaction (Reactant, Product)
ID    Attribute    ReactionStoichiometry    String    Identifier shortname of the reaction
Stoichiometry    Attribute    ReactionStoichiometry    String    Stoichiometry of the reaction
Substrate    Attribute    ReactionStoichiometry    String    Identifier shortname of a substrate
Product    Attribute    ReactionStoichiometry    String    Identifier shortname of a product
Location    Attribute    ReactionStoichiometry    String    Compartment in which the reaction occurs
Reaction    Attribute    ReactionStoichiometry    String    
RowNumber    Attribute    SparseMatrixOrdered    Integer    Number of row
ColumnNumber    Attribute    SparseMatrixOrdered    Integer    Number of column
Value    Attribute    SparseMatrixOrdered    Float    Value
RowID    Attribute    SparseMatrix    String    Row identifier
ColumnID    Attribute    SparseMatrix    String    Column identifier
Value    Attribute    SparseMatrix    Float    Value
RowID    Attribute    SparseMatrixRow    String    Row identifier
RowString    Attribute    SparseMatrixRow    String    JSON string describing all elements in the row
ColumnID    Attribute    SparseMatrixColumn    String    Column identifier
ColumnString    Attribute    SparseMatrixColumn    String    JSON string describing all elements in the column
ID    Attribute    Relationship    String    
FromObject    Attribute    Relationship    String    
ToObject    Attribute    Relationship    String    
Value    Attribute    Relationship    Integer    
IsSymmetric    Attribute    Relationship    Boolean    
Sign    Attribute    Relationship    Enum(['+', '-', '0'], default='0')    
Relation    Attribute    Relationship    String    
Element    Attribute    Position    String    
PositionX    Attribute    Position    Float    
PositionY    Attribute    Position    Float