Class: Parameter

URI: tvbo:Parameter

 classDiagram
    class Parameter
    click Parameter href "./Parameter.html"
      Parameter <|-- DerivedParameter
        click DerivedParameter href "./DerivedParameter.html"
      
      Parameter : comment
        
          
    
        
        
        Parameter --> "0..1" String : comment
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

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

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

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

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

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

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

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

        
      Parameter : element_domains
        
          
    
        
        
        Parameter --> "*" Range : element_domains
        click Range href "./Range.html"
    

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

        
      Parameter : explored_values
        
          
    
        
        
        Parameter --> "*" Float : explored_values
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

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

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

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

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

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

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

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

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

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

        
      Parameter : source
        
          
    
        
        
        Parameter --> "0..1" Uriorcurie : source
        click Uriorcurie href "../http://www.w3.org/2001/XMLSchema#anyURI.html"
    

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

        
      Parameter : unit
        
          
    
        
        
        Parameter --> "0..1" UnitEnum : unit
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Parameter : value
        
          
    
        
        
        Parameter --> "0..1" ScalarValue : value
        click ScalarValue href "./ScalarValue.html"
    

        
      

Inheritance

• Parameter
  • DerivedParameter

Class Properties

Property	Value
Class URI	tvbo:Parameter

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string	Globally unique identifier for the entity	direct
label	0..1 xsd:string		direct
symbol	0..1 xsd:string		direct
definition	0..1 xsd:string		direct
value	0..1 ScalarValue	Numeric, string, or boolean value, OR an array (nested list) for array-valued…	direct
default	0..1 xsd:string		direct
domain	0..1 Range		direct
reported_optimum	0..1 xsd:float		direct
description	0..1 xsd:string		direct
equation	0..1 Equation		direct
unit	0..1 UnitEnum	Physical unit of measurement	direct
dataset_path	0..1 xsd:string	Dataset path for array-valued parameters	direct
grounding	* xsd:anyURI	External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this enti…	direct
comment	0..1 xsd:string		direct
heterogeneous	0..1 xsd:boolean		direct
distribution	0..1 Distribution	Distribution for heterogeneous per-node parameter sampling	direct
source	0..1 xsd:anyURI	Data source for this parameter’s value	direct
measure	0..1 xsd:string	Selector into the source	direct
free	0..1 xsd:boolean		direct
shape	0..1 xsd:string		direct
explored_values	* xsd:float		direct
element_domains	* Range	Per-element domain overrides for heterogeneous parameters	direct
datatype	0..1 xsd:string	Declared value type of this parameter, given as a schema range name — a primi…	direct
required	0..1 xsd:boolean	Whether a value for this parameter must be supplied	direct

Usages

used by	used in	type	used
StimulationSetting	amplitude	range	Parameter
StimulationSetting	frequency	range	Parameter
StimulationSetting	pulse_width	range	Parameter
Equation	parameters	range	Parameter
Stimulus	parameters	range	Parameter
Event	parameters	range	Parameter
TemporalApplicableEquation	parameters	range	Parameter
Network	parameters	range	Parameter
GraphGenerator	parameters	range	Parameter
Node	parameters	range	Parameter
Edge	parameters	range	Parameter
Observation	parameters	range	Parameter
Analysis	parameters	range	Parameter
Dynamics	parameters	range	Parameter
Dynamics	coupling_terms	range	Parameter
Dynamics	local_coupling_term	range	Parameter
Distribution	parameters	range	Parameter
Noise	parameters	range	Parameter
Noise	intensity	range	Parameter
OptimizationStage	hyperparameters	range	Parameter
OptimizationStage	freeze_parameters	range	Parameter
Optimization	hyperparameters	range	Parameter
Optimization	freeze_parameters	range	Parameter
Exploration	parameters	range	Parameter
ExplorationAxis	parameter	range	Parameter
FreeParameter	parameter	range	Parameter
UpdateRule	target_parameter	range	Parameter
AlgorithmInclude	arguments	range	Parameter
AlgorithmStage	arguments	range	Parameter
Algorithm	hyperparameters	range	Parameter
Discretization	parameters	range	Parameter
BranchSwitch	parameters	range	Parameter
Continuation	free_parameters	range	Parameter
Integrator	parameters	range	Parameter
Coupling	parameters	range	Parameter
DifferentialOperator	coefficient	range	Parameter
DifferentialOperator	tensor_coefficient	range	Parameter
PDE	parameters	range	Parameter

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

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

LinkML Source

Direct

name: Parameter
from_schema: https://w3id.org/tvbo
slots:
- name
- label
- symbol
- definition
- value
- default
- domain
- reported_optimum
- description
- equation
- unit
- dataset_path
- grounding
attributes:
  comment:
    name: comment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:comment
    domain_of:
    - Parameter
    range: string
  heterogeneous:
    name: heterogeneous
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    - FreeParameter
    range: boolean
  distribution:
    name: distribution
    description: Distribution for heterogeneous per-node parameter sampling. Implies
      heterogeneous=true.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  source:
    name: source
    description: Data source for this parameter's value. When set, the value is loaded
      from the referenced entity rather than being a YAML literal. The referent is
      typically a Network with per-node parameters (dscalar pattern) or a flat dataset
      (HDF5, TSV). Combine with `measure:` when the source exposes multiple named
      measures. Distinct from the global `iri:` slot, which is reserved for ontology
      grounding.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Edge
    - Observation
    - Dynamics
    - Parameter
    - CouplingInput
    - Likelihood
    range: uriorcurie
    required: false
  measure:
    name: measure
    description: Selector into the source. When `source` points at a Network with
      per-node parameters (or a dscalar with multiple maps), picks which named measure
      to load. Aligns with names listed in Network.structural_measures / Network.observational_measures.
      Ignored when the source resolves to a scalar/array dataset.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    range: string
    required: false
  free:
    name: free
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    range: boolean
  shape:
    name: shape
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Matrix
    - NamedArray
    - Parameter
    - FreeParameter
    - NDArray
    range: string
  explored_values:
    name: explored_values
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Range
    - Parameter
    - ExplorationAxis
    range: float
    multivalued: true
  element_domains:
    name: element_domains
    description: Per-element domain overrides for heterogeneous parameters. When specified,
      element_domains[i] overrides domain for element i during exploration auto-expansion.
      Length must match parameter shape (e.g., n_nodes for shape "(n_nodes,)"). If
      not set, all elements share the same domain.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    - ExplorationAxis
    range: Range
    multivalued: true
    inlined_as_list: true
  datatype:
    name: datatype
    description: Declared value type of this parameter, given as a schema range name
      — a primitive (``integer``, ``float``, ``string``, ``uriorcurie``) or a class
      (e.g. ``Distribution``). Documents the expected type when the parameter is a
      *declaration* carrying no concrete ``value`` (e.g. a GraphGenerator's typed
      argument interface). Distinct from ``domain`` (numeric bounds) and ``unit``.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    range: string
  required:
    name: required
    description: Whether a value for this parameter must be supplied. Optional parameters
      (e.g. a generator's ``seed``) set this to false. Declaration metadata; unset
      means unconstrained.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Parameter
    range: boolean
class_uri: tvbo:Parameter

Induced

name: Parameter
from_schema: https://w3id.org/tvbo
attributes:
  comment:
    name: comment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:comment
    owner: Parameter
    domain_of:
    - Parameter
    range: string
  heterogeneous:
    name: heterogeneous
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    - FreeParameter
    range: boolean
  distribution:
    name: distribution
    description: Distribution for heterogeneous per-node parameter sampling. Implies
      heterogeneous=true.
    from_schema: https://w3id.org/tvbo
    owner: Parameter
    domain_of:
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  source:
    name: source
    description: Data source for this parameter's value. When set, the value is loaded
      from the referenced entity rather than being a YAML literal. The referent is
      typically a Network with per-node parameters (dscalar pattern) or a flat dataset
      (HDF5, TSV). Combine with `measure:` when the source exposes multiple named
      measures. Distinct from the global `iri:` slot, which is reserved for ontology
      grounding.
    from_schema: https://w3id.org/tvbo
    owner: Parameter
    domain_of:
    - Edge
    - Observation
    - Dynamics
    - Parameter
    - CouplingInput
    - Likelihood
    range: uriorcurie
    required: false
  measure:
    name: measure
    description: Selector into the source. When `source` points at a Network with
      per-node parameters (or a dscalar with multiple maps), picks which named measure
      to load. Aligns with names listed in Network.structural_measures / Network.observational_measures.
      Ignored when the source resolves to a scalar/array dataset.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: string
    required: false
  free:
    name: free
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: boolean
  shape:
    name: shape
    from_schema: https://w3id.org/tvbo
    owner: Parameter
    domain_of:
    - Matrix
    - NamedArray
    - Parameter
    - FreeParameter
    - NDArray
    range: string
  explored_values:
    name: explored_values
    from_schema: https://w3id.org/tvbo
    owner: Parameter
    domain_of:
    - Range
    - Parameter
    - ExplorationAxis
    range: float
    multivalued: true
  element_domains:
    name: element_domains
    description: Per-element domain overrides for heterogeneous parameters. When specified,
      element_domains[i] overrides domain for element i during exploration auto-expansion.
      Length must match parameter shape (e.g., n_nodes for shape "(n_nodes,)"). If
      not set, all elements share the same domain.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    - ExplorationAxis
    range: Range
    multivalued: true
    inlined: true
    inlined_as_list: true
  datatype:
    name: datatype
    description: Declared value type of this parameter, given as a schema range name
      — a primitive (``integer``, ``float``, ``string``, ``uriorcurie``) or a class
      (e.g. ``Distribution``). Documents the expected type when the parameter is a
      *declaration* carrying no concrete ``value`` (e.g. a GraphGenerator's typed
      argument interface). Distinct from ``domain`` (numeric bounds) and ``unit``.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: string
  required:
    name: required
    description: Whether a value for this parameter must be supplied. Optional parameters
      (e.g. a generator's ``seed``) set this to false. Declaration metadata; unset
      means unconstrained.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: boolean
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: Parameter
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Event
    - Tractogram
    - 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
    range: string
    required: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: Parameter
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - 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
  symbol:
    name: symbol
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - StateVariable
    - Parameter
    - DerivedParameter
    - DerivedVariable
    range: string
  definition:
    name: definition
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: skos:definition
    owner: Parameter
    domain_of:
    - Equation
    - StateVariable
    - Parameter
    - Function
    - DifferentialOperator
    range: string
  value:
    name: value
    description: Numeric, string, or boolean value, OR an array (nested list) for
      array-valued constants such as mode-coupling coefficient matrices. ScalarValue
      accepts any literal primitive type, allowing parameters to carry control flags
      (e.g., booleans) or symbolic placeholders alongside numeric defaults.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: schema:value
    owner: Parameter
    domain_of:
    - StateValue
    - Parameter
    - Argument
    - Option
    - BoundaryCondition
    range: ScalarValue
    any_of:
    - range: ScalarValue
  default:
    name: default
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: schema:defaultValue
    owner: Parameter
    domain_of:
    - Parameter
    range: string
  domain:
    name: domain
    from_schema: https://w3id.org/tvbo
    aliases:
    - range
    - boundaries
    rank: 1000
    owner: Parameter
    domain_of:
    - ClinicalScale
    - ClinicalScore
    - StateVariable
    - Distribution
    - Parameter
    - ExplorationAxis
    - FreeParameter
    - PDE
    range: Range
  reported_optimum:
    name: reported_optimum
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: float
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: Parameter
    domain_of:
    - Dataset
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - 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
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  equation:
    name: equation
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: tvbo:Equation
    owner: Parameter
    domain_of:
    - Stimulus
    - Event
    - ProcedureStep
    - Observation
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - Case
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    range: Equation
    inlined: true
  unit:
    name: unit
    description: Physical unit of measurement. Values are drawn from the QUDT ontology
      (http://qudt.org/vocab/unit/) with UO cross-references where available.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: qudt:unit
    owner: Parameter
    domain_of:
    - CommonCoordinateSpace
    - MeasureSpec
    - NamedArray
    - Edge
    - StateVariable
    - Parameter
    - Argument
    - DerivedParameter
    - DerivedVariable
    - ExplorationAxis
    - Integrator
    - TimeSeries
    - NDArray
    - SpatialField
    range: UnitEnum
  dataset_path:
    name: dataset_path
    description: Dataset path for array-valued parameters. When set, the parameter
      value is stored in the binary companion file (HDF5 or Zarr) at this path. The
      value slot is omitted.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Parameter
    domain_of:
    - Parameter
    range: string
  grounding:
    name: grounding
    description: 'External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that
      this entity is a surrogate / abstraction / model of. Replaces the legacy OWL
      pattern `tvbo:surrogate_of` by carrying the link 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: oboInOwl:hasDbXref
    owner: Parameter
    domain_of:
    - StateVariable
    - Parameter
    - DerivedVariable
    range: uriorcurie
    multivalued: true
class_uri: tvbo:Parameter