SigPath

Package org.sigpath.bioimport.reaction2

Class Summary
BindingDeclaration indicates that the requirement deals with a constant.
BindingDeclarationDescriptor Class BindingDeclarationDescriptor.
Change_log Used to annotate change log information, including who submitted this record, when the record was submitted, and when the record was last modified.
Change_logDescriptor Class Change_logDescriptor.
Compartment Class Compartment.
CompartmentDescriptor Class CompartmentDescriptor.
Complex element used to define a complex in SigPath
ComplexDescriptor Class ComplexDescriptor.
Components Groups complex and modified chemical definitions in SigPath
ComponentsDescriptor Class ComponentsDescriptor.
Concentration_measurement Used to describe concentration measurements for molecules in SigPath
Concentration_measurementDescriptor Class Concentration_measurementDescriptor.
Concentration_measurements Groups concentration measurements in SigPath
Concentration_measurementsDescriptor Class Concentration_measurementsDescriptor.
CustomKinetic Class CustomKinetic.
CustomKineticDescriptor Class CustomKineticDescriptor.
EnzymaticParameters Groups the parameters of an enzymatic reaction in SigPath
EnzymaticParametersDescriptor Class EnzymaticParametersDescriptor.
EnzymaticReaction element used to encapsulate data defining an enzymatic reaction in SigPath
EnzymaticReactionDescriptor Class EnzymaticReactionDescriptor.
Enzyme Identifies the enzyme for an enzymatic reaction
EnzymeDescriptor Class EnzymeDescriptor.
ExcludedReaction Class ExcludedReaction.
ExcludedReactionDescriptor Class ExcludedReactionDescriptor.
ExcludedReactions Class ExcludedReactions.
ExcludedReactionsDescriptor Class ExcludedReactionsDescriptor.
ExternalReference Annotates external references.
ExternalReferenceDescriptor Class ExternalReferenceDescriptor.
Formula can be an expression like k*p1*p2, but also a numerical value (0 for instance)
FormulaDescriptor Class FormulaDescriptor.
InContactWith Class InContactWith.
InContactWithDescriptor Class InContactWithDescriptor.
InteractionRef Used to reference an interaction.
InteractionRefDescriptor Class InteractionRefDescriptor.
InternalLinks Used to describe internal links within SigPath
InternalLinksDescriptor Class InternalLinksDescriptor.
InvolvedInReaction Used to list reactions that a molecule is involved in by spid (unique SigPath identifier)
InvolvedInReactionDescriptor Class InvolvedInReactionDescriptor.
KBackward Defines the KBackward value for a basic reaction
KBackwardDescriptor Class KBackwardDescriptor.
KBKP Defines the KBKP value for an enzymatic reaction
KBKPDescriptor Class KBKPDescriptor.
KForward Defines the KForward value for a basic reaction
KForwardDescriptor Class KForwardDescriptor.
Kinetic This element declares a new type of kinetic.
KineticBindings name to constant/chemical elements
KineticBindingsDescriptor Class KineticBindingsDescriptor.
KineticDescriptor Class KineticDescriptor.
KineticRef there are two way to define a kinetic, either indicating a class which realizes a specified kinetic, either indication a kinetic declaration, also part of the submission
KineticRefDescriptor Class KineticRefDescriptor.
Kinetics group of kinetics declaration in SigPath
KineticsDescriptor Class KineticsDescriptor.
KMichaelis Defines the KMichaelis value for an enzymatic reaction
KMichaelisDescriptor Class KMichaelisDescriptor.
Kp Defines the Kp (KCat) value for an enzymatic reaction
KpDescriptor Class KpDescriptor.
Left Contains molecules on the left side of a reaction
LeftDescriptor Class LeftDescriptor.
Location Allows you to locate a molecule in one or more compartment if null compatible old data
LocationDescriptor Class LocationDescriptor.
Model encapsulates data defining a model
ModelCompartments Groups compartments of a model
ModelCompartmentsDescriptor Class ModelCompartmentsDescriptor.
ModelConcentration Selects molecule concentrations in a model
ModelConcentrationDescriptor Class ModelConcentrationDescriptor.
ModelDescriptor Class ModelDescriptor.
ModelReaction Used to identify a reaction within a model
ModelReactionDescriptor Class ModelReactionDescriptor.
ModifiedChemical Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath.
ModifiedChemicalDescriptor Class ModifiedChemicalDescriptor.
Modifiers Contains molecules that influence the velocities of the reaction
ModifiersDescriptor Class ModifiersDescriptor.
Molecule Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac.
MoleculeConcentration Defines the initial concentration of a molecule in a model
MoleculeConcentrationDescriptor Class MoleculeConcentrationDescriptor.
MoleculeDescriptor Class MoleculeDescriptor.
MoleculeExcluded Class MoleculeExcluded.
MoleculeExcludedDescriptor Class MoleculeExcludedDescriptor.
NamedChemical Annotates a SigPath chemical with a name but no accession code
NamedChemicalDescriptor Class NamedChemicalDescriptor.
NamedChemicalInteraction Annotates an interaction between two named-chemicals in SigPath.
NamedChemicalInteractionDescriptor Class NamedChemicalInteractionDescriptor.
NamedChemicalInteractions Groups named-chemical-interaction definitions in SigPath
NamedChemicalInteractionsDescriptor Class NamedChemicalInteractionsDescriptor.
NamedChemicalRef The reference value of a named chemical.
NamedChemicalRefDescriptor Class NamedChemicalRefDescriptor.
NamedChemicals Groups named-chemical definitions in SigPath
NamedChemicalsDescriptor Class NamedChemicalsDescriptor.
OnLeft Class OnLeft.
OnLeftDescriptor Class OnLeftDescriptor.
OnRight Class OnRight.
OnRightDescriptor Class OnRightDescriptor.
Organism Organism of origin for a protein
OrganismDescriptor Class OrganismDescriptor.
Parameter Defines the any parameter
ParameterBinding binds a name (a common parametername as Kf) with a parameter.
ParameterBindingDescriptor Class ParameterBindingDescriptor.
ParameterDescriptor Class ParameterDescriptor.
Parameters Groups the parameters of a reaction in SigPath
ParametersBindingsDeclaration can be an expression like k*p1*p2, but also a numerical value (0 for instance)
ParametersBindingsDeclarationDescriptor Class ParametersBindingsDeclarationDescriptor.
ParametersDescriptor Class ParametersDescriptor.
Pathway encapsulates data defining a pathway
PathwayDescriptor Class PathwayDescriptor.
PathwayReaction Used to identify a reaction within a pathway
PathwayReactionDescriptor Class PathwayReactionDescriptor.
Pending_item Defines a pending item
Pending_itemDescriptor Class Pending_itemDescriptor.
Pending_list Defines a list of pending items
Pending_listDescriptor Class Pending_listDescriptor.
Pending_reviews Groups pending reviews
Pending_reviewsDescriptor Class Pending_reviewsDescriptor.
PreviousVersion previous version of a sigpathEntity
PreviousVersionDescriptor Class PreviousVersionDescriptor.
Protein element used to define a protein in SigPath
ProteinDescriptor Class ProteinDescriptor.
Proteins Groups protein definitions in SigPath
ProteinsDescriptor Class ProteinsDescriptor.
Publications Annotates publications in relation to a reaction or molecule concentration
PublicationsDescriptor Class PublicationsDescriptor.
Reaction element used to encapsulate data defining a reaction in SigPath
ReactionDescriptor Class ReactionDescriptor.
Ref annotates a reference which has a PubMed ID
RefDescriptor Class RefDescriptor.
Review Used to annotate a SigPath review, including review description, who conducted the review, and date/time review was conducted.
ReviewDescriptor Class ReviewDescriptor.
Reviews Used to annotate SigPath reviews
ReviewsDescriptor Class ReviewsDescriptor.
Right Contains molecules on the right side of a reaction
RightDescriptor Class RightDescriptor.
SigpathSubmission Root element used to encapsulate data for SigPath Export or Import
SigpathSubmissionDescriptor Class SigpathSubmissionDescriptor.
SmallMolecule element used to define a small molecule in SigPath
SmallMoleculeDescriptor Class SmallMoleculeDescriptor.
SmallMolecules Groups small molecule definitions in SigPath
SmallMoleculesDescriptor Class SmallMoleculesDescriptor.
Source Class Source.
SourceDescriptor Class SourceDescriptor.
SpeciesBinding binds a name(usually the function of the chemical) with a chemical.
SpeciesBindingDescriptor Class SpeciesBindingDescriptor.
SpeciesBindingsDeclaration can be an expression like k*p1*p2, but also a numerical value (0 for instance)
SpeciesBindingsDeclarationDescriptor Class SpeciesBindingsDeclarationDescriptor.
TargetUnit Selects the concentration units required for creating/submitting a model
TargetUnitDescriptor Class TargetUnitDescriptor.
UserComment Annotates a SigPath user-comment
UserCommentDescriptor Class UserCommentDescriptor.
UserComments Groups user-comment
UserCommentsDescriptor Class UserCommentsDescriptor.
VMax Defines the Vmax value for an enzymatic reaction
VMax_EnzymeConcentration The concentration of the enzyme used to measure the value of VMax.
VMax_EnzymeConcentrationDescriptor Class VMax_EnzymeConcentrationDescriptor.
VMaxDescriptor Class VMaxDescriptor.
 


SigPath

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