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SigPath | |||||||||
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.action | |
|---|---|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.action.biowizard | |
|---|---|
| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
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| Pathway
encapsulates data defining a pathway |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.action.edit | |
|---|---|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.bioimport | |
|---|---|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.bioimport.reaction2 | |
|---|---|
| BindingDeclaration
indicates that the requirement deals with a constant. |
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| 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. |
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| Compartment
Class Compartment. |
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| Complex
element used to define a complex in SigPath |
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| Components
Groups complex and modified chemical definitions in SigPath |
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| Concentration_measurement
Used to describe concentration measurements for molecules in SigPath |
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| Concentration_measurements
Groups concentration measurements in SigPath |
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| CustomKinetic
Class CustomKinetic. |
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| EnzymaticParameters
Groups the parameters of an enzymatic reaction in SigPath |
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| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
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| Enzyme
Identifies the enzyme for an enzymatic reaction |
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| ExcludedReaction
Class ExcludedReaction. |
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| ExcludedReactions
Class ExcludedReactions. |
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| ExternalReference
Annotates external references. |
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| Formula
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| InContactWith
Class InContactWith. |
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| InteractionRef
Used to reference an interaction. |
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| InternalLinks
Used to describe internal links within SigPath |
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| InvolvedInReaction
Used to list reactions that a molecule is involved in by spid (unique SigPath identifier) |
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| KBackward
Defines the KBackward value for a basic reaction |
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| KBKP
Defines the KBKP value for an enzymatic reaction |
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| KForward
Defines the KForward value for a basic reaction |
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| Kinetic
This element declares a new type of kinetic. |
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| KineticBindings
name to constant/chemical elements |
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| 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 |
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| Kinetics
group of kinetics declaration in SigPath |
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| KMichaelis
Defines the KMichaelis value for an enzymatic reaction |
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| Kp
Defines the Kp (KCat) value for an enzymatic reaction |
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| Left
Contains molecules on the left side of a reaction |
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| Location
Allows you to locate a molecule in one or more compartment if null compatible old data |
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| Model
encapsulates data defining a model |
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| ModelCompartments
Groups compartments of a model |
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| ModelConcentration
Selects molecule concentrations in a model |
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| ModelReaction
Used to identify a reaction within a model |
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| ModifiedChemical
Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. |
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| Modifiers
Contains molecules that influence the velocities of the reaction |
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| 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. |
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| MoleculeConcentration
Defines the initial concentration of a molecule in a model |
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| MoleculeExcluded
Class MoleculeExcluded. |
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| NamedChemical
Annotates a SigPath chemical with a name but no accession code |
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| NamedChemicalInteraction
Annotates an interaction between two named-chemicals in SigPath. |
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| NamedChemicalInteractions
Groups named-chemical-interaction definitions in SigPath |
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| NamedChemicalRef
The reference value of a named chemical. |
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| NamedChemicals
Groups named-chemical definitions in SigPath |
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| OnLeft
Class OnLeft. |
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| OnRight
Class OnRight. |
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| Organism
Organism of origin for a protein |
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| Parameter
Defines the any parameter |
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| ParameterBinding
binds a name (a common parametername as Kf) with a parameter. |
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| Parameters
Groups the parameters of a reaction in SigPath |
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| ParametersBindingsDeclaration
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| Pathway
encapsulates data defining a pathway |
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| PathwayReaction
Used to identify a reaction within a pathway |
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| Pending_item
Defines a pending item |
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| Pending_list
Defines a list of pending items |
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| Pending_reviews
Groups pending reviews |
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| PreviousVersion
previous version of a sigpathEntity |
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| Protein
element used to define a protein in SigPath |
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| Proteins
Groups protein definitions in SigPath |
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| Publications
Annotates publications in relation to a reaction or molecule concentration |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| Ref
annotates a reference which has a PubMed ID |
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| Review
Used to annotate a SigPath review, including review description, who conducted the review, and date/time review was conducted. |
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| Reviews
Used to annotate SigPath reviews |
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| Right
Contains molecules on the right side of a reaction |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| SmallMolecule
element used to define a small molecule in SigPath |
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| SmallMolecules
Groups small molecule definitions in SigPath |
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| Source
Class Source. |
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| SpeciesBinding
binds a name(usually the function of the chemical) with a chemical. |
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| SpeciesBindingsDeclaration
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| TargetUnit
Selects the concentration units required for creating/submitting a model |
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| UserComment
Annotates a SigPath user-comment |
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| UserComments
Groups user-comment |
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| VMax
Defines the Vmax value for an enzymatic reaction |
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| VMax_EnzymeConcentration
The concentration of the enzyme used to measure the value of VMax. |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.navigator.memorystore | |
|---|---|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry | |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.components | |
|---|---|
| UserComments
Groups user-comment |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.model | |
|---|---|
| Compartment
Class Compartment. |
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| ExcludedReaction
Class ExcludedReaction. |
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| Model
encapsulates data defining a model |
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| ModelConcentration
Selects molecule concentrations in a model |
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| ModelReaction
Used to identify a reaction within a model |
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| 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. |
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| MoleculeConcentration
Defines the initial concentration of a molecule in a model |
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| MoleculeExcluded
Class MoleculeExcluded. |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.pages | |
|---|---|
| Kinetic
This element declares a new type of kinetic. |
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| KineticBindings
name to constant/chemical elements |
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| NamedChemical
Annotates a SigPath chemical with a name but no accession code |
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| Publications
Annotates publications in relation to a reaction or molecule concentration |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| Ref
annotates a reference which has a PubMed ID |
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| UserComment
Annotates a SigPath user-comment |
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| UserComments
Groups user-comment |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.pages.model | |
|---|---|
| Compartment
Class Compartment. |
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| ExcludedReaction
Class ExcludedReaction. |
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| Model
encapsulates data defining a model |
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| ModelConcentration
Selects molecule concentrations in a model |
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| ModelReaction
Used to identify a reaction within a model |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.pages.reactions | |
|---|---|
| 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. |
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| Publications
Annotates publications in relation to a reaction or molecule concentration |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.tapestry.util | |
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| ModelReaction
Used to identify a reaction within a model |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task | |
|---|---|
| Pathway
encapsulates data defining a pathway |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.model | |
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| Model
encapsulates data defining a model |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.navigator | |
|---|---|
| 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. |
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| Concentration_measurement
Used to describe concentration measurements for molecules in SigPath |
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| CustomKinetic
Class CustomKinetic. |
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| EnzymaticParameters
Groups the parameters of an enzymatic reaction in SigPath |
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| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
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| Enzyme
Identifies the enzyme for an enzymatic reaction |
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| ExcludedReactions
Class ExcludedReactions. |
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| Formula
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| InteractionRef
Used to reference an interaction. |
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| Kinetic
This element declares a new type of kinetic. |
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| KineticBindings
name to constant/chemical elements |
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| 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 |
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| Left
Contains molecules on the left side of a reaction |
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| Model
encapsulates data defining a model |
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| ModelCompartments
Groups compartments of a model |
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| ModelReaction
Used to identify a reaction within a model |
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| ModifiedChemical
Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. |
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| Modifiers
Contains molecules that influence the velocities of the reaction |
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| 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. |
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| NamedChemicalInteraction
Annotates an interaction between two named-chemicals in SigPath. |
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| NamedChemicalRef
The reference value of a named chemical. |
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| Parameters
Groups the parameters of a reaction in SigPath |
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| ParametersBindingsDeclaration
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| Pending_list
Defines a list of pending items |
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| PreviousVersion
previous version of a sigpathEntity |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| Reviews
Used to annotate SigPath reviews |
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| Right
Contains molecules on the right side of a reaction |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| SpeciesBindingsDeclaration
can be an expression like k*p1*p2, but also a numerical value (0 for instance) |
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| TargetUnit
Selects the concentration units required for creating/submitting a model |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.navigator.export | |
|---|---|
| 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. |
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| Complex
element used to define a complex in SigPath |
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| Concentration_measurement
Used to describe concentration measurements for molecules in SigPath |
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| CustomKinetic
Class CustomKinetic. |
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| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
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| ExternalReference
Annotates external references. |
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| Kinetic
This element declares a new type of kinetic. |
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| Model
encapsulates data defining a model |
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| ModifiedChemical
Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. |
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| NamedChemical
Annotates a SigPath chemical with a name but no accession code |
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| NamedChemicalInteraction
Annotates an interaction between two named-chemicals in SigPath. |
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| Organism
Organism of origin for a protein |
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| Pathway
encapsulates data defining a pathway |
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| Pending_list
Defines a list of pending items |
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| Protein
element used to define a protein in SigPath |
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| Publications
Annotates publications in relation to a reaction or molecule concentration |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| Ref
annotates a reference which has a PubMed ID |
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| Reviews
Used to annotate SigPath reviews |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| SmallMolecule
element used to define a small molecule in SigPath |
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| UserComment
Annotates a SigPath user-comment |
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| UserComments
Groups user-comment |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.navigator.save | |
|---|---|
| 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. |
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| Complex
element used to define a complex in SigPath |
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| Concentration_measurement
Used to describe concentration measurements for molecules in SigPath |
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| CustomKinetic
Class CustomKinetic. |
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| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
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| Kinetic
This element declares a new type of kinetic. |
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| Model
encapsulates data defining a model |
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| ModifiedChemical
Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. |
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| NamedChemical
Annotates a SigPath chemical with a name but no accession code |
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| NamedChemicalInteraction
Annotates an interaction between two named-chemicals in SigPath. |
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| Organism
Organism of origin for a protein |
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| Pathway
encapsulates data defining a pathway |
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| Pending_list
Defines a list of pending items |
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| Protein
element used to define a protein in SigPath |
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| Reaction
element used to encapsulate data defining a reaction in SigPath |
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| Ref
annotates a reference which has a PubMed ID |
|
| SmallMolecule
element used to define a small molecule in SigPath |
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| UserComment
Annotates a SigPath user-comment |
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| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.util | |
|---|---|
| Compartment
Class Compartment. |
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| ExcludedReactions
Class ExcludedReactions. |
|
| Kinetic
This element declares a new type of kinetic. |
|
| KineticBindings
name to constant/chemical elements |
|
| Location
Allows you to locate a molecule in one or more compartment if null compatible old data |
|
| Model
encapsulates data defining a model |
|
| ModelCompartments
Groups compartments of a model |
|
| MoleculeConcentration
Defines the initial concentration of a molecule in a model |
|
| TargetUnit
Selects the concentration units required for creating/submitting a model |
|
| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.xml | |
|---|---|
| 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. |
|
| Components
Groups complex and modified chemical definitions in SigPath |
|
| Concentration_measurement
Used to describe concentration measurements for molecules in SigPath |
|
| CustomKinetic
Class CustomKinetic. |
|
| EnzymaticParameters
Groups the parameters of an enzymatic reaction in SigPath |
|
| EnzymaticReaction
element used to encapsulate data defining an enzymatic reaction in SigPath |
|
| ExcludedReaction
Class ExcludedReaction. |
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| ExcludedReactions
Class ExcludedReactions. |
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| ExternalReference
Annotates external references. |
|
| InteractionRef
Used to reference an interaction. |
|
| Kinetic
This element declares a new type of kinetic. |
|
| Model
encapsulates data defining a model |
|
| ModelCompartments
Groups compartments of a model |
|
| 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. |
|
| NamedChemical
Annotates a SigPath chemical with a name but no accession code |
|
| NamedChemicalInteraction
Annotates an interaction between two named-chemicals in SigPath. |
|
| Parameters
Groups the parameters of a reaction in SigPath |
|
| Pathway
encapsulates data defining a pathway |
|
| PathwayReaction
Used to identify a reaction within a pathway |
|
| Pending_reviews
Groups pending reviews |
|
| Protein
element used to define a protein in SigPath |
|
| Publications
Annotates publications in relation to a reaction or molecule concentration |
|
| Reaction
element used to encapsulate data defining a reaction in SigPath |
|
| Reviews
Used to annotate SigPath reviews |
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| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
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| SmallMolecule
element used to define a small molecule in SigPath |
|
| TargetUnit
Selects the concentration units required for creating/submitting a model |
|
| UserComments
Groups user-comment |
|
| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.task.xml.export | |
|---|---|
| ModifiedChemical
Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. |
|
| Publications
Annotates publications in relation to a reaction or molecule concentration |
|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
|
| Classes in org.sigpath.bioimport.reaction2 used by org.sigpath.util.xml | |
|---|---|
| SigpathSubmission
Root element used to encapsulate data for SigPath Export or Import |
|
|
SigPath | |||||||||
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