Class: DerivedObservation

Observation derived from one or more other observations. Examples: - fc (from bold) - single source transformation - fc_corr (from fc and fc_target) - multi-source comparison Unlike regular Observations, these don’t generate monitor classes but are computed from existing observation values.

URI: tvbo:DerivedObservation

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

        
      DerivedObservation : aggregation
        
          
    
        
        
        DerivedObservation --> "0..1" AggregationType : aggregation
        click AggregationType href "../../enums/AggregationType.html"
    

        
      DerivedObservation : class_reference
        
          
    
        
        
        DerivedObservation --> "0..1" ClassReference : class_reference
        click ClassReference href "./ClassReference.html"
    

        
      DerivedObservation : data_source
        
          
    
        
        
        DerivedObservation --> "0..1" DataSource : data_source
        click DataSource href "./DataSource.html"
    

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

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

        
      DerivedObservation : environment
        
          
    
        
        
        DerivedObservation --> "0..1" SoftwareEnvironment : environment
        click SoftwareEnvironment href "./SoftwareEnvironment.html"
    

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

        
      DerivedObservation : imaging_modality
        
          
    
        
        
        DerivedObservation --> "0..1" ImagingModality : imaging_modality
        click ImagingModality href "../../enums/ImagingModality.html"
    

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

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

        
      DerivedObservation : parameters
        
          
    
        
        
        DerivedObservation --> "*" Parameter : parameters
        click Parameter href "./Parameter.html"
    

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

        
      DerivedObservation : pipeline
        
          
    
        
        
        DerivedObservation --> "*" FunctionCall : pipeline
        click FunctionCall href "./FunctionCall.html"
    

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

        
      DerivedObservation : source
        
          
    
        
        
        DerivedObservation --> "0..1" StateVariable : source
        click StateVariable href "./StateVariable.html"
    

        
      DerivedObservation : source_observations
        
          
    
        
        
        DerivedObservation --> "1..*" Observation : source_observations
        click Observation href "./Observation.html"
    

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

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

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

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

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

        
      

Inheritance

• Observation
  • DerivedObservation

Slots

Name	Cardinality and Range	Description	Inheritance
source_observations	1..* Observation	One or more observations to derive from	direct
name	1 xsd:string		Observation
acronym	0..1 xsd:string		Observation
label	0..1 xsd:string		Observation
description	0..1 xsd:string		Observation
equation	0..1 Equation		Observation
parameters	* Parameter		Observation
environment	0..1 SoftwareEnvironment		Observation
time_scale	0..1 xsd:string		Observation
source	0..1 StateVariable	State variable to observe (e	Observation
period	0..1 xsd:float	Sampling period for monitors (ms)	Observation
downsample_period	0..1 xsd:float	Intermediate downsampling period (ms)	Observation
voi	0..1 xsd:integer	Variable of interest index (which state variable to monitor)	Observation
imaging_modality	0..1 ImagingModality	Type of imaging modality (BOLD, EEG, MEG, etc	Observation
warmup_source	0..1 xsd:string	Reference to transient simulation result for history initialization (e	Observation
data_source	0..1 DataSource	Load data from external source (file, database, API)	Observation
skip_t	0..1 xsd:integer	Number of samples to skip at the start (transient removal)	Observation
tail_samples	0..1 xsd:integer	Number of samples from the end to use	Observation
aggregation	0..1 AggregationType	How to aggregate over time	Observation
window_size	0..1 xsd:integer	Number of samples for windowed aggregation	Observation
pipeline	* FunctionCall	Ordered sequence of Functions	Observation
class_reference	0..1 ClassReference	Direct class reference (alternative to pipeline)	Observation

Usages

used by	used in	type	used
SimulationExperiment	derived_observations	range	DerivedObservation

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

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

LinkML Source

Direct

name: DerivedObservation
description: 'Observation derived from one or more other observations. Examples: -
  fc (from bold) - single source transformation - fc_corr (from fc and fc_target)
  - multi-source comparison Unlike regular Observations, these don''t generate monitor
  classes but are computed from existing observation values.'
from_schema: https://w3id.org/tvbo
is_a: Observation
attributes:
  source_observations:
    name: source_observations
    description: One or more observations to derive from. For transformations (e.g.,
      fc from bold), use single source. For comparisons (e.g., fc_corr from fc and
      fc_target), use multiple sources. Order may matter for asymmetric operations.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - DerivedObservation
    range: Observation
    required: true
    multivalued: true
    inlined: false
    minimum_cardinality: 1
class_uri: tvbo:DerivedObservation

Induced

name: DerivedObservation
description: 'Observation derived from one or more other observations. Examples: -
  fc (from bold) - single source transformation - fc_corr (from fc and fc_target)
  - multi-source comparison Unlike regular Observations, these don''t generate monitor
  classes but are computed from existing observation values.'
from_schema: https://w3id.org/tvbo
is_a: Observation
attributes:
  source_observations:
    name: source_observations
    description: One or more observations to derive from. For transformations (e.g.,
      fc from bold), use single source. For comparisons (e.g., fc_corr from fc and
      fc_target), use multiple sources. Order may matter for asymmetric operations.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: source_observations
    owner: DerivedObservation
    domain_of:
    - DerivedObservation
    range: Observation
    required: true
    multivalued: true
    inlined: false
    minimum_cardinality: 1
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    key: true
    alias: name
    owner: DerivedObservation
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - Tractogram
    - File
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - Algorithm
    - Coupling
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    range: string
    required: true
  acronym:
    name: acronym
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: acronym
    owner: DerivedObservation
    domain_of:
    - ClinicalScale
    - ClinicalScore
    - Observation
    - Function
    range: string
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: DerivedObservation
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: description
    owner: DerivedObservation
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Tractogram
    - Matrix
    - Network
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - 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
    alias: equation
    owner: DerivedObservation
    domain_of:
    - Stimulus
    - Observation
    - StateVariable
    - Distribution
    - Parameter
    - Function
    - Case
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    range: Equation
    inlined: true
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: parameters
    owner: DerivedObservation
    domain_of:
    - Equation
    - Stimulus
    - TemporalApplicableEquation
    - Node
    - Edge
    - Observation
    - Dynamics
    - Distribution
    - Noise
    - Exploration
    - Integrator
    - Coupling
    - PDE
    range: Parameter
    multivalued: true
    inlined: true
  environment:
    name: environment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: environment
    owner: DerivedObservation
    domain_of:
    - Observation
    - SimulationExperiment
    - PDESolver
    range: SoftwareEnvironment
  time_scale:
    name: time_scale
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: ms
    alias: time_scale
    owner: DerivedObservation
    domain_of:
    - Observation
    - Integrator
    range: string
  source:
    name: source
    description: State variable to observe (e.g., S_e for excitatory activity). For
      observations derived from other observations, use DerivedObservation.
    from_schema: https://w3id.org/tvbo
    alias: source
    owner: DerivedObservation
    domain_of:
    - Edge
    - Observation
    - Dynamics
    range: StateVariable
    inlined: false
  period:
    name: period
    description: 'Sampling period for monitors (ms). For BOLD: TR in ms.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: period
    owner: DerivedObservation
    domain_of:
    - Observation
    range: float
  downsample_period:
    name: downsample_period
    description: 'Intermediate downsampling period (ms). For BOLD: typically matches
      dt.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: downsample_period
    owner: DerivedObservation
    domain_of:
    - Observation
    range: float
  voi:
    name: voi
    description: 'Variable of interest index (which state variable to monitor). Default:
      0.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: voi
    owner: DerivedObservation
    domain_of:
    - Observation
    range: integer
  imaging_modality:
    name: imaging_modality
    description: Type of imaging modality (BOLD, EEG, MEG, etc.)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: imaging_modality
    owner: DerivedObservation
    domain_of:
    - Observation
    range: ImagingModality
  warmup_source:
    name: warmup_source
    description: Reference to transient simulation result for history initialization
      (e.g., 'result_init').
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: warmup_source
    owner: DerivedObservation
    domain_of:
    - Observation
    - ClassReference
    range: string
  data_source:
    name: data_source
    description: Load data from external source (file, database, API). When specified,
      this observation represents empirical/external data rather than simulated data.
      Enables unified treatment of all data.
    from_schema: https://w3id.org/tvbo
    alias: data_source
    owner: DerivedObservation
    domain_of:
    - Parcellation
    - Tractogram
    - Observation
    range: DataSource
    inlined: true
  skip_t:
    name: skip_t
    description: 'Number of samples to skip at the start (transient removal). For
      FC: typically 10-20 TRs.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: skip_t
    owner: DerivedObservation
    domain_of:
    - Observation
    range: integer
  tail_samples:
    name: tail_samples
    description: 'Number of samples from the end to use. Takes the last N samples
      before aggregation. E.g., tail_samples: 500 means use data[-500:].'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: tail_samples
    owner: DerivedObservation
    domain_of:
    - Observation
    range: integer
  aggregation:
    name: aggregation
    description: How to aggregate over time
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: aggregation
    owner: DerivedObservation
    domain_of:
    - Observation
    - Coupling
    range: AggregationType
  window_size:
    name: window_size
    description: Number of samples for windowed aggregation
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: window_size
    owner: DerivedObservation
    domain_of:
    - Observation
    range: integer
  pipeline:
    name: pipeline
    description: Ordered sequence of Functions. Each Function transforms input → output.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: pipeline
    owner: DerivedObservation
    domain_of:
    - Observation
    range: FunctionCall
    multivalued: true
    inlined: true
    inlined_as_list: true
  class_reference:
    name: class_reference
    description: 'Direct class reference (alternative to pipeline). Use for external
      library classes like tvboptim.Bold, custom monitors, or any callable class.
      The class is instantiated with constructor_args and called with call_args. Example:
      {name: Bold, module: tvboptim.observations.tvb_monitors.bold, constructor_args:
      [{name: period, value: 1000.0}]}'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: class_reference
    owner: DerivedObservation
    domain_of:
    - Observation
    range: ClassReference
    inlined: true
class_uri: tvbo:DerivedObservation