Class: StateVariable

URI: tvbo:StateVariable

 classDiagram
    class StateVariable
    click StateVariable href "./StateVariable.html"
      StateVariable <|-- FieldStateVariable
        click FieldStateVariable href "./FieldStateVariable.html"
      
      StateVariable : coupling_variable
        
          
    
        
        
        StateVariable --> "0..1" Boolean : coupling_variable
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      StateVariable : definition
        
          
    
        
        
        StateVariable --> "0..1" String : definition
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : derivative_initial_value
        
          
    
        
        
        StateVariable --> "0..1" Float : derivative_initial_value
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      StateVariable : description
        
          
    
        
        
        StateVariable --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : distribution
        
          
    
        
        
        StateVariable --> "0..1" Distribution : distribution
        click Distribution href "./Distribution.html"
    

        
      StateVariable : domain
        
          
    
        
        
        StateVariable --> "0..1" Range : domain
        click Range href "./Range.html"
    

        
      StateVariable : equation
        
          
    
        
        
        StateVariable --> "0..1" Equation : equation
        click Equation href "./Equation.html"
    

        
      StateVariable : equation_order
        
          
    
        
        
        StateVariable --> "0..1" Integer : equation_order
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      StateVariable : equation_type
        
          
    
        
        
        StateVariable --> "0..1" String : equation_type
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : evict_equation
        
          
    
        
        
        StateVariable --> "0..1" Equation : evict_equation
        click Equation href "./Equation.html"
    

        
      StateVariable : grounding
        
          
    
        
        
        StateVariable --> "*" Uriorcurie : grounding
        click Uriorcurie href "../http://www.w3.org/2001/XMLSchema#anyURI.html"
    

        
      StateVariable : history
        
          
    
        
        
        StateVariable --> "0..1" TimeSeries : history
        click TimeSeries href "./TimeSeries.html"
    

        
      StateVariable : initial_value
        
          
    
        
        
        StateVariable --> "0..1" Float : initial_value
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      StateVariable : label
        
          
    
        
        
        StateVariable --> "0..1" String : label
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : name
        
          
    
        
        
        StateVariable --> "1" String : name
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : noise
        
          
    
        
        
        StateVariable --> "0..1" Noise : noise
        click Noise href "./Noise.html"
    

        
      StateVariable : record
        
          
    
        
        
        StateVariable --> "0..1" Boolean : record
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      StateVariable : stimulation_variable
        
          
    
        
        
        StateVariable --> "0..1" Boolean : stimulation_variable
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      StateVariable : symbol
        
          
    
        
        
        StateVariable --> "0..1" String : symbol
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : unit
        
          
    
        
        
        StateVariable --> "0..1" String : unit
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StateVariable : variable_of_interest
        
          
    
        
        
        StateVariable --> "0..1" Boolean : variable_of_interest
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"

Inheritance

Class Properties

Property Value
Class URI tvbo:StateVariable

Slots

Name Cardinality and Range Description Inheritance
name 1
xsd:string		 Globally unique identifier for the entity direct
symbol 0..1
xsd:string		 direct
label 0..1
xsd:string		 direct
definition 0..1
xsd:string		 direct
domain 0..1
Range		 direct
description 0..1
xsd:string		 direct
equation 0..1
Equation		 direct
unit 0..1
xsd:string or 
UnitEnum		 Physical unit of measurement direct
record 0..1
xsd:boolean		 Whether to include this element in simulation output files direct
grounding *
xsd:anyURI		 External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this enti… direct
variable_of_interest 0..1
xsd:boolean		 direct
coupling_variable 0..1
xsd:boolean		 Whether this state variable is transmitted to connected nodes through the cou… direct
equation_type 0..1
xsd:string		 How to interpret ``equation direct
evict_equation 0..1
Equation		 Optional reverse recurrence for a sliding-window reduction: the per-step … direct
equation_order 0..1
xsd:integer		 Order of the time derivative on the LHS direct
noise 0..1
Noise		 direct
stimulation_variable 0..1
xsd:boolean		 direct
initial_value 0..1
xsd:float		 Value this state starts at direct
derivative_initial_value 0..1
xsd:float		 Initial value for the first time derivative, used when equation_order > 1 direct
distribution 0..1
Distribution		 Distribution for sampling initial conditions per node direct
history 0..1
TimeSeries		 direct

Usages

used by used in type used
Observation source any_of[range] StateVariable
Dynamics state_variables range StateVariable
Noise targets range StateVariable
TuningObjective target_variable range StateVariable
Coupling incoming_states range StateVariable
Coupling local_states range StateVariable

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/tvbo

Mappings

Mapping Type Mapped Value
self tvbo:StateVariable
native tvbo:StateVariable

LinkML Source

Direct

name: StateVariable
from_schema: https://w3id.org/tvbo
slots:
- name
- symbol
- label
- definition
- domain
- description
- equation
- unit
- record
- grounding
slot_usage:
  record:
    name: record
    ifabsent: 'True'
attributes:
  variable_of_interest:
    name: variable_of_interest
    deprecated: Use 'record' instead. A state variable is recorded in the output when
      record=true (the default); set record=false to suppress it. 'variable_of_interest'
      is retained for backward compatibility and is ignored by the TVB/jax/rateml
      codegen.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    domain_of:
    - StateVariable
    range: boolean
  coupling_variable:
    name: coupling_variable
    description: Whether this state variable is transmitted to connected nodes through
      the coupling function. In TVB terms, this determines the cvar indices (state
      variables extracted from history and fed into the coupling function). The coupling
      function may override this via its incoming_states attribute.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    domain_of:
    - StateVariable
    range: boolean
  equation_type:
    name: equation_type
    description: 'How to interpret ``equation.rhs`` when advancing this state: ''differential''
      (default) integrates it as ``dx/dt = rhs``; ''algebraic'' is a constraint ``0
      = rhs`` / ``x ~ rhs`` (DAE); ''recurrence'' is a discrete per-step update ``x_next
      = rhs`` (no integrator applied), used by an observation''s auxiliary ``dynamics``
      for online reductions/accumulators (e.g. a running sum ``x_next = x + f``) —
      the symbolic, backend-independent sibling of the continuous ''differential''
      form. Algebraic equations are used by ModelingToolkit.jl backend.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(differential)
    domain_of:
    - StateVariable
    range: string
  evict_equation:
    name: evict_equation
    description: 'Optional reverse recurrence for a **sliding-window** reduction:
      the per-step downdate that removes the sample leaving the window, the inverse
      of ``equation`` (which folds an arriving sample in). Only meaningful when ``equation_type:
      recurrence`` on an observation''s auxiliary ``dynamics``. When present, the
      observer is a windowed reduction — its state is maintained by ``equation`` (add)
      and ``evict_equation`` (evict) and rebuilt exactly from the window on resync
      — rather than a cumulative accumulator over the whole trajectory (``equation``
      alone). Absent for ordinary state variables and cumulative reductions.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StateVariable
    range: Equation
  equation_order:
    name: equation_order
    description: Order of the time derivative on the LHS. Default 1 means dx/dt =
      rhs (first-order ODE). Order 2 means d²x/dt² = rhs (second-order ODE), etc.
      Higher-order ODEs are automatically lowered to coupled first-order systems by
      backends like ModelingToolkit.jl via mtkcompile.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: int(1)
    domain_of:
    - StateVariable
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  stimulation_variable:
    name: stimulation_variable
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StateVariable
    range: boolean
  initial_value:
    name: initial_value
    description: 'Value this state starts at. Absent means undeclared: the consumer
      supplies its own fallback via ``tvbo.utils.initial_value``, which documents
      why this slot carries no schema default.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StateVariable
    - FreeParameter
    - SpatialField
    range: float
  derivative_initial_value:
    name: derivative_initial_value
    description: Initial value for the first time derivative, used when equation_order
      > 1. For a second-order ODE d²x/dt² = f, this sets dx/dt(0). Required by ModelingToolkit.jl
      to fully specify higher-order initial value problems.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StateVariable
    range: float
  distribution:
    name: distribution
    description: Distribution for sampling initial conditions per node. If present,
      initial_value is used as fallback/mean.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - ProcedureStep
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  history:
    name: history
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StateVariable
    range: TimeSeries
    inlined: true
class_uri: tvbo:StateVariable

Induced

name: StateVariable
from_schema: https://w3id.org/tvbo
slot_usage:
  record:
    name: record
    ifabsent: 'True'
attributes:
  variable_of_interest:
    name: variable_of_interest
    deprecated: Use 'record' instead. A state variable is recorded in the output when
      record=true (the default); set record=false to suppress it. 'variable_of_interest'
      is retained for backward compatibility and is ignored by the TVB/jax/rateml
      codegen.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    owner: StateVariable
    domain_of:
    - StateVariable
    range: boolean
  coupling_variable:
    name: coupling_variable
    description: Whether this state variable is transmitted to connected nodes through
      the coupling function. In TVB terms, this determines the cvar indices (state
      variables extracted from history and fed into the coupling function). The coupling
      function may override this via its incoming_states attribute.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    owner: StateVariable
    domain_of:
    - StateVariable
    range: boolean
  equation_type:
    name: equation_type
    description: 'How to interpret ``equation.rhs`` when advancing this state: ''differential''
      (default) integrates it as ``dx/dt = rhs``; ''algebraic'' is a constraint ``0
      = rhs`` / ``x ~ rhs`` (DAE); ''recurrence'' is a discrete per-step update ``x_next
      = rhs`` (no integrator applied), used by an observation''s auxiliary ``dynamics``
      for online reductions/accumulators (e.g. a running sum ``x_next = x + f``) —
      the symbolic, backend-independent sibling of the continuous ''differential''
      form. Algebraic equations are used by ModelingToolkit.jl backend.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(differential)
    owner: StateVariable
    domain_of:
    - StateVariable
    range: string
  evict_equation:
    name: evict_equation
    description: 'Optional reverse recurrence for a **sliding-window** reduction:
      the per-step downdate that removes the sample leaving the window, the inverse
      of ``equation`` (which folds an arriving sample in). Only meaningful when ``equation_type:
      recurrence`` on an observation''s auxiliary ``dynamics``. When present, the
      observer is a windowed reduction — its state is maintained by ``equation`` (add)
      and ``evict_equation`` (evict) and rebuilt exactly from the window on resync
      — rather than a cumulative accumulator over the whole trajectory (``equation``
      alone). Absent for ordinary state variables and cumulative reductions.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - StateVariable
    range: Equation
  equation_order:
    name: equation_order
    description: Order of the time derivative on the LHS. Default 1 means dx/dt =
      rhs (first-order ODE). Order 2 means d²x/dt² = rhs (second-order ODE), etc.
      Higher-order ODEs are automatically lowered to coupled first-order systems by
      backends like ModelingToolkit.jl via mtkcompile.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: int(1)
    owner: StateVariable
    domain_of:
    - StateVariable
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    owner: StateVariable
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  stimulation_variable:
    name: stimulation_variable
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - StateVariable
    range: boolean
  initial_value:
    name: initial_value
    description: 'Value this state starts at. Absent means undeclared: the consumer
      supplies its own fallback via ``tvbo.utils.initial_value``, which documents
      why this slot carries no schema default.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - StateVariable
    - FreeParameter
    - SpatialField
    range: float
  derivative_initial_value:
    name: derivative_initial_value
    description: Initial value for the first time derivative, used when equation_order
      > 1. For a second-order ODE d²x/dt² = f, this sets dx/dt(0). Required by ModelingToolkit.jl
      to fully specify higher-order initial value problems.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - StateVariable
    range: float
  distribution:
    name: distribution
    description: Distribution for sampling initial conditions per node. If present,
      initial_value is used as fallback/mean.
    from_schema: https://w3id.org/tvbo
    owner: StateVariable
    domain_of:
    - ProcedureStep
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  history:
    name: history
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - StateVariable
    range: TimeSeries
    inlined: true
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: StateVariable
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Event
    - Tractogram
    - ResultEntity
    - Activity
    - CachedArray
    - MeasureSpec
    - NamedArray
    - GraphGenerator
    - Binding
    - ProcedureStep
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - EnvironmentVariable
    - SchedulerDirective
    - Reducer
    range: string
    required: true
  symbol:
    name: symbol
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StateVariable
    domain_of:
    - ToolUnit
    - StateVariable
    - Parameter
    - CouplingInput
    - DerivedParameter
    - DerivedVariable
    range: string
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: StateVariable
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - Figure
    - Panel
    - Inset
    - Layer
    - Colorbar
    - Rule
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Phenotype
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - AlgorithmStage
    - TuningObjective
    - Continuation
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  definition:
    name: definition
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: skos:definition
    owner: StateVariable
    domain_of:
    - Equation
    - StateVariable
    - Parameter
    - Function
    - DifferentialOperator
    range: string
  domain:
    name: domain
    from_schema: https://w3id.org/tvbo
    aliases:
    - range
    - boundaries
    rank: 1000
    owner: StateVariable
    domain_of:
    - ClinicalScale
    - ClinicalScore
    - StateVariable
    - Distribution
    - Parameter
    - ExplorationAxis
    - FreeParameter
    - PDE
    range: Range
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: StateVariable
    domain_of:
    - CommonCoordinateSpace
    - Dataset
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - ResultEntity
    - Activity
    - Phenotype
    - MeasureSpec
    - NamedArray
    - Network
    - GraphGenerator
    - ProcedureStep
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - AlgorithmStage
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - Study
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    - Reducer
    range: string
  equation:
    name: equation
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: tvbo:Equation
    owner: StateVariable
    domain_of:
    - Stimulus
    - Event
    - ProcedureStep
    - Observation
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    - BoundaryCondition
    range: Equation
    inlined: true
  unit:
    name: unit
    description: 'Physical unit of measurement. `UnitEnum` is the curated vocabulary
      — each of its values is vendored from QUDT (`ontology/tvb-o-units.ttl`) and
      can be reasoned about dimensionally. The range is deliberately open beyond it:
      a unit nobody has curated yet is recorded as written and reported `uncurated`,
      because a closed range forces the author to either misdeclare the quantity or
      leave it undeclared, and both lose more than an unrecognised string does. An
      uncurated unit carries no dimensional claim, so a check involving it reports
      `underdetermined` rather than guessing. Promote one with `tvbo units add <unit>`,
      which pulls its QUDT record into the vendored module — so every unit TVBO *reasons*
      about stays authoritative, and only what it *records* is open.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: qudt:unit
    owner: StateVariable
    domain_of:
    - CommonCoordinateSpace
    - ToolUnit
    - MeasureSpec
    - NamedArray
    - Edge
    - Observation
    - StateVariable
    - Parameter
    - Argument
    - DerivedParameter
    - DerivedVariable
    - ExplorationAxis
    - Integrator
    - TimeSeries
    - NDArray
    - SpatialField
    range: string
    any_of:
    - range: UnitEnum
    - range: string
  record:
    name: record
    description: Whether to include this element in simulation output files. Applicable
      to state variables (default true), derived variables (default false), and network
      nodes (default true). On an observation it forces (true) or suppresses (false)
      persistence in the result; left unset, a terminal observation (one not consumed
      by another observation or a loss) is recorded and an intermediate one is not.
      Set false to suppress recording.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    owner: StateVariable
    domain_of:
    - Node
    - Observation
    - StateVariable
    - DerivedVariable
    - Exploration
    range: boolean
  grounding:
    name: grounding
    description: 'External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that
      this entity is a surrogate / abstraction / model of. Realized as the `tvbo:surrogate_of`
      object property, carried inline with the YAML data instance. Multiple IRIs allowed:
      a single parameter may abstract several biological processes (e.g. a synaptic
      conductance grounding both GO:0060079 (excitatory PSP) and GO:0007268 (chemical
      synaptic transmission)).'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: tvbo:surrogate_of
    owner: StateVariable
    domain_of:
    - StateVariable
    - Parameter
    - DerivedVariable
    range: uriorcurie
    multivalued: true
class_uri: tvbo:StateVariable