Class: Observation

Unified class for all observation/measurement specifications. Covers monitors (BOLD, EEG), tuning observables, and derived quantities. Pipeline is a sequence of Functions with input → output flow.

URI: tvbo:Observation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Inheritance

Slots

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

Usages

used by used in type used
DerivedObservation source_observations range Observation
UpdateRule requires range Observation
TuningObjective target_data range Observation
Algorithm observations range Observation
SimulationExperiment observations range Observation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Observation
description: Unified class for all observation/measurement specifications. Covers
  monitors (BOLD, EEG), tuning observables, and derived quantities. Pipeline is a
  sequence of Functions with input → output flow.
from_schema: https://w3id.org/tvbo
slots:
- name
- acronym
- label
- description
- equation
- parameters
- environment
- time_scale
attributes:
  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
    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
    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
    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
    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
    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
    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
    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
    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
    domain_of:
    - Observation
    range: integer
  aggregation:
    name: aggregation
    description: How to aggregate over time
    from_schema: https://w3id.org/tvbo
    rank: 1000
    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
    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
    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
    domain_of:
    - Observation
    range: ClassReference
    inlined: true
class_uri: tvbo:Observation

Induced

name: Observation
description: Unified class for all observation/measurement specifications. Covers
  monitors (BOLD, EEG), tuning observables, and derived quantities. Pipeline is a
  sequence of Functions with input → output flow.
from_schema: https://w3id.org/tvbo
attributes:
  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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    domain_of:
    - Observation
    range: ClassReference
    inlined: true
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    key: true
    alias: name
    owner: Observation
    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: Observation
    domain_of:
    - ClinicalScale
    - ClinicalScore
    - Observation
    - Function
    range: string
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    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: Observation
    domain_of:
    - Observation
    - Integrator
    range: string
class_uri: tvbo:Observation