Class: DerivedParameter

URI: tvbo:DerivedParameter

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Inheritance

Class Properties

Property Value
Class URI tvbo:DerivedParameter

Slots

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

Usages

used by used in type used
Dynamics derived_parameters range DerivedParameter
PDE derived_parameters range DerivedParameter

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: DerivedParameter
from_schema: https://w3id.org/tvbo
is_a: Parameter
slots:
- name
- symbol
- description
- equation
- unit
class_uri: tvbo:DerivedParameter

Induced

name: DerivedParameter
from_schema: https://w3id.org/tvbo
is_a: Parameter
attributes:
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: DerivedParameter
    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
  symbol:
    name: symbol
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: DerivedParameter
    domain_of:
    - StateVariable
    - Parameter
    - DerivedParameter
    - DerivedVariable
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    domain_of:
    - CommonCoordinateSpace
    - MeasureSpec
    - NamedArray
    - Edge
    - StateVariable
    - Parameter
    - Argument
    - DerivedParameter
    - DerivedVariable
    - ExplorationAxis
    - Integrator
    - TimeSeries
    - NDArray
    - SpatialField
    range: UnitEnum
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: DerivedParameter
    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
  definition:
    name: definition
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: skos:definition
    owner: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    domain_of:
    - Parameter
    range: string
  domain:
    name: domain
    from_schema: https://w3id.org/tvbo
    aliases:
    - range
    - boundaries
    rank: 1000
    owner: DerivedParameter
    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: DerivedParameter
    domain_of:
    - Parameter
    range: float
  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: DerivedParameter
    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: DerivedParameter
    domain_of:
    - StateVariable
    - Parameter
    - DerivedVariable
    range: uriorcurie
    multivalued: true
  comment:
    name: comment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:comment
    owner: DerivedParameter
    domain_of:
    - Parameter
    range: string
  heterogeneous:
    name: heterogeneous
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    domain_of:
    - Parameter
    range: string
    required: false
  free:
    name: free
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: DerivedParameter
    domain_of:
    - Parameter
    range: boolean
  shape:
    name: shape
    from_schema: https://w3id.org/tvbo
    owner: DerivedParameter
    domain_of:
    - Matrix
    - NamedArray
    - Parameter
    - FreeParameter
    - NDArray
    range: string
  explored_values:
    name: explored_values
    from_schema: https://w3id.org/tvbo
    owner: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    domain_of:
    - Parameter
    range: boolean
class_uri: tvbo:DerivedParameter