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

        
      DerivedParameter : used
        
          
    
        
        
        DerivedParameter --> "0..1" DataRef : used
        click DataRef href "./DataRef.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
xsd:string or 
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
grounding *
xsd:anyURI		 External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this enti… Parameter
producer 0..1
FunctionCall		 HOW to compute this value, when it is derived rather than obtained — the call… 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		 WHERE this parameter’s value comes from — a curated entity’s IRI, or a path (… Parameter
measure 0..1
xsd:string		 WHICH array to select out of source Parameter
used 0..1
DataRef		 WHERE + WHICH + SLICE in one edge — this parameter’s array sourced from anoth… 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
    - 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: DerivedParameter
    domain_of:
    - ToolUnit
    - StateVariable
    - Parameter
    - CouplingInput
    - DerivedParameter
    - DerivedVariable
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: DerivedParameter
    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: DerivedParameter
    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: DerivedParameter
    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
  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
    - 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: DerivedParameter
    domain_of:
    - Equation
    - StateVariable
    - Parameter
    - Function
    - DifferentialOperator
    range: string
  value:
    name: value
    annotations:
      simple_dict_value:
        tag: simple_dict_value
        value: true
    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:
    - Digest
    - StateValue
    - Parameter
    - Argument
    - Option
    - EnvironmentVariable
    - SchedulerDirective
    - ResultBinding
    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
  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: DerivedParameter
    domain_of:
    - StateVariable
    - Parameter
    - DerivedVariable
    range: uriorcurie
    multivalued: true
  producer:
    name: producer
    description: 'HOW to compute this value, when it is derived rather than obtained
      — the callable that produces it, its arguments, and (via `output:`) which entry
      to take from a callable returning several named arrays. The callable resolves
      against the recipe''s `code_source`. Use instead of `source:` for a value that
      is a deterministic function of the spec''s own inputs (a mesh operator, a template
      matrix): declaring the producer keeps the spec the single source of truth, where
      pointing at a pre-built file would let the two drift apart silently — and would
      need a prep step run by hand before the spec could execute. The result is cached
      and invalidated by the artifact fingerprint, so it is computed once rather than
      per run. On a `Parameter` it produces the value; on an `Edge` it produces the
      whole template matrix, which is what lets a connectome or a discrete differential
      operator be declared rather than pre-built. Mutually exclusive with `value:`/`source:`.'
    from_schema: https://w3id.org/tvbo
    close_mappings:
    - prov:wasGeneratedBy
    rank: 1000
    owner: DerivedParameter
    domain_of:
    - Edge
    - Parameter
    range: FunctionCall
    required: false
    inlined: true
  comment:
    name: comment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:comment
    owner: DerivedParameter
    domain_of:
    - Parameter
    - WorkflowEngineConfig
    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:
    - ProcedureStep
    - StateVariable
    - Parameter
    - Noise
    - Prior
    - Coupling
    range: Distribution
    inlined: true
  source:
    name: source
    description: 'WHERE this parameter''s value comes from — a curated entity''s IRI,
      or a path (resolved against the declaring spec''s directory when relative, as
      `Network.bids_dir` / `Network.data_file` are). The referent is typically a Network
      with per-node parameters (dscalar pattern) or a binary store (HDF5, Zarr, TSV).
      Combine with `measure:` to pick one array out of a source that holds several.
      A sourced value is never inlined into generated code: it is resolved lazily
      and the backend reads it from storage, so an array of any size costs nothing
      in the spec or the emitted module. Mutually exclusive with `value:` (a YAML
      literal, which IS materialised) and with `producer:` (bytes that are computed
      rather than read). Distinct from the global `iri:` slot, which is reserved for
      ontology grounding.'
    from_schema: https://w3id.org/tvbo
    owner: DerivedParameter
    domain_of:
    - Panel
    - Edge
    - Observation
    - Dynamics
    - Parameter
    - CouplingInput
    - Likelihood
    - ResultBinding
    range: uriorcurie
    required: false
  measure:
    name: measure
    description: 'WHICH array to select out of `source`. The address space is the
      source''s own: a per-node measure name for a Network (aligning with Network.structural_measures
      / observational_measures), a dataset key for an HDF5/Zarr store, a recorded
      measure for an experiment result. Omit when the source resolves to a single
      array.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: DerivedParameter
    domain_of:
    - Parameter
    range: string
    required: false
  used:
    name: used
    description: WHERE + WHICH + SLICE in one edge — this parameter's array sourced
      from another experiment's result (an operating point, a tuned ``estimate__<name>``
      a fit persisted), a dataset, or a curated entity, PROV ``prov:used``. The full
      cross-container form of which `source:`+`measure:` is the no-``sel``/no-``experiment``
      shorthand; adds label ``reconcile`` and a swept-point ``sel``. Like `source:`
      the array is resolved lazily and never inlined. An in-study ``experiment`` reference
      also registers the workflow dependency. Mutually exclusive with `value:`/`source:`/`producer:`.
    from_schema: https://w3id.org/tvbo
    slot_uri: prov:used
    owner: DerivedParameter
    domain_of:
    - Layer
    - Annotation
    - Activity
    - Parameter
    - Argument
    - ResultBinding
    range: DataRef
    inlined: true
  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
    - CachedArray
    - 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