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 : 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 : analysis
        
          
    
        
        
        Observation --> "0..1" Analysis : analysis
        click Analysis href "./Analysis.html"
    

        
      Observation : aux_data
        
          
    
        
        
        Observation --> "*" Reference : aux_data
        click Reference href "./Reference.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 --> "*" String : source
        click String href "../http://www.w3.org/2001/XMLSchema#string.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" UnitEnum : time_scale
        click UnitEnum href "../../enums/UnitEnum.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"
    

        
      

Class Properties

Property	Value
Class URI	tvbo:Observation

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string	Globally unique identifier for the entity	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 UnitEnum	Time unit for the integration / simulation	direct
source	* xsd:string or  StateVariable or  Observation	Ordered list of inputs this observation derives from	direct
aux_data	* Reference	Ordered list of auxiliary inputs the observation pipeline consumes	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
analysis	0..1 Analysis	Marks this observation as an analysis observable that operates on the solve/l…	direct

Usages

used by	used in	type	used
Observation	source	any_of[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: Ordered list of inputs this observation derives from. Each entry
      is either a StateVariable reference (raw observation of an integrated trajectory,
      e.g. ``S_e``) or an Observation reference (derived observation, e.g. ``bold``).
      Codegen checks each source name against ``experiment.observations``; names matching
      an existing observation flag the parent as derived.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Edge
    - Observation
    - Dynamics
    - Parameter
    - CouplingInput
    - Likelihood
    multivalued: true
    inlined: false
    any_of:
    - range: StateVariable
    - range: Observation
  aux_data:
    name: aux_data
    description: 'Ordered list of auxiliary inputs the observation pipeline consumes.
      Examples: a Surface mesh''s faces array, an empirical FC matrix on a reference
      Network, or another Observation''s output. Resolved load-time eagerly; rendered
      code is self-contained.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Observation
    range: Reference
    multivalued: true
    inlined: true
    inlined_as_list: true
  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 step has a unique `name` (used
      to key step outputs) and transforms input -> output. List form preserves execution
      order.
    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
  analysis:
    name: analysis
    description: Marks this observation as an analysis observable that operates on
      the solve/loss rather than a result-data pipeline (autodiff gradient, finite-difference
      gradient, or Lyapunov spectrum).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Observation
    range: Analysis
    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: Ordered list of inputs this observation derives from. Each entry
      is either a StateVariable reference (raw observation of an integrated trajectory,
      e.g. ``S_e``) or an Observation reference (derived observation, e.g. ``bold``).
      Codegen checks each source name against ``experiment.observations``; names matching
      an existing observation flag the parent as derived.
    from_schema: https://w3id.org/tvbo
    owner: Observation
    domain_of:
    - Edge
    - Observation
    - Dynamics
    - Parameter
    - CouplingInput
    - Likelihood
    range: string
    multivalued: true
    inlined: false
    any_of:
    - range: StateVariable
    - range: Observation
  aux_data:
    name: aux_data
    description: 'Ordered list of auxiliary inputs the observation pipeline consumes.
      Examples: a Surface mesh''s faces array, an empirical FC matrix on a reference
      Network, or another Observation''s output. Resolved load-time eagerly; rendered
      code is self-contained.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Observation
    domain_of:
    - Observation
    range: Reference
    multivalued: true
    inlined: true
    inlined_as_list: true
  period:
    name: period
    description: 'Sampling period for monitors (ms). For BOLD: TR in ms.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    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
    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
    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
    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
    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
    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
    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
    owner: Observation
    domain_of:
    - Observation
    range: integer
  aggregation:
    name: aggregation
    description: How to aggregate over time
    from_schema: https://w3id.org/tvbo
    rank: 1000
    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
    owner: Observation
    domain_of:
    - Observation
    range: integer
  pipeline:
    name: pipeline
    description: Ordered sequence of Functions. Each step has a unique `name` (used
      to key step outputs) and transforms input -> output. List form preserves execution
      order.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    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
    owner: Observation
    domain_of:
    - Observation
    range: ClassReference
    inlined: true
  analysis:
    name: analysis
    description: Marks this observation as an analysis observable that operates on
      the solve/loss rather than a result-data pipeline (autodiff gradient, finite-difference
      gradient, or Lyapunov spectrum).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Observation
    domain_of:
    - Observation
    range: Analysis
    inlined: true
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: Observation
    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
  acronym:
    name: acronym
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: skos:notation
    owner: Observation
    domain_of:
    - ClinicalScale
    - ClinicalScore
    - Observation
    - Function
    - FunctionCall
    range: string
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: Observation
    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
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: Observation
    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: Observation
    domain_of:
    - Stimulus
    - Event
    - ProcedureStep
    - Observation
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - Case
    - DerivedParameter
    - DerivedVariable
    - Noise
    - UpdateRule
    - DifferentialOperator
    range: Equation
    inlined: true
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Observation
    domain_of:
    - Equation
    - Stimulus
    - Event
    - TemporalApplicableEquation
    - Network
    - GraphGenerator
    - Node
    - Edge
    - Observation
    - Analysis
    - Dynamics
    - Distribution
    - Noise
    - Exploration
    - Discretization
    - BranchSwitch
    - Integrator
    - Coupling
    - PDE
    range: Parameter
    multivalued: true
    inlined: true
  environment:
    name: environment
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Observation
    domain_of:
    - Observation
    - SimulationExperiment
    - PDESolver
    range: SoftwareEnvironment
  time_scale:
    name: time_scale
    description: Time unit for the integration / simulation. Determines the physical
      time meaning of one model time-step.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: ms
    owner: Observation
    domain_of:
    - Observation
    - Integrator
    range: UnitEnum
class_uri: tvbo:Observation