Class: Phenotype

Per-subject phenotype table (BIDS phenotype/ directory convention). Carries cognitive scores, clinical scales, demographic variables, behavioral task outputs, physiological measures, or any other per-subject numeric measurement bundle for a cohort. Sidecar companion to per-subject Network sidecars in multi-subject studies that correlate simulated quantities with empirical scores (e.g. PMAT24_A, g-factor, CardSort, ProcSpeed for Schirner 2023). The yaml carries metadata + the measure list; the h5 carries measures/<name> 1-D float arrays of length len(subjects).

Aligns with the BIDS phenotype standard (https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files/phenotypic-and-assessment-data.html) and with NIDM’s nidm:Phenotype concept. Per-measure metadata can optionally carry Cognitive Atlas (https://www.cognitiveatlas.org/) cogat:Task and cogat:Concept IRIs via measure_specs.

URI: tvbo:Phenotype

 classDiagram
    class Phenotype
    click Phenotype href "./Phenotype.html"
      Phenotype : category
        
          
    
        
        
        Phenotype --> "0..1" String : category
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

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

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

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

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

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

        
      Phenotype : measure_specs
        
          
    
        
        
        Phenotype --> "*" MeasureSpec : measure_specs
        click MeasureSpec href "./MeasureSpec.html"
    

        
      Phenotype : measures
        
          
    
        
        
        Phenotype --> "*" String : measures
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Phenotype : provenance
        
          
    
        
        
        Phenotype --> "0..1" Provenance : provenance
        click Provenance href "./Provenance.html"
    

        
      Phenotype : subjects
        
          
    
        
        
        Phenotype --> "1..*" String : subjects
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"

Class Properties

Property Value
Class URI tvbo:Phenotype

Slots

Name Cardinality and Range Description Inheritance
label 0..1
xsd:string		 direct
description 0..1
xsd:string		 direct
dataset_id 1
xsd:string		 Unique identifier for this phenotype bundle direct
subjects 1..*
xsd:string		 Ordered list of subject IDs (e direct
measures *
xsd:string		 Names of the measures present in the h5 companion (one measures/<name> da… direct
measure_specs *
MeasureSpec		 Optional per-measure metadata (Cognitive Atlas IRIs, units, description) direct
category 0..1
xsd:string		 Coarse classification of the phenotype bundle, used for filtering in larger s… direct
data_file 1
xsd:string		 Path to the h5 companion (relative to the yaml) direct
cohort 0..1
xsd:string		 Cohort label (e direct
provenance 0..1
Provenance		 W3C PROV-O metadata for the source of these scores direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Phenotype
description: 'Per-subject phenotype table (BIDS ``phenotype/`` directory convention).
  Carries cognitive scores, clinical scales, demographic variables, behavioral task
  outputs, physiological measures, or any other per-subject numeric measurement bundle
  for a cohort. Sidecar companion to per-subject Network sidecars in multi-subject
  studies that correlate simulated quantities with empirical scores (e.g. PMAT24_A,
  g-factor, CardSort, ProcSpeed for Schirner 2023). The yaml carries metadata + the
  measure list; the h5 carries ``measures/<name>`` 1-D float arrays of length ``len(subjects)``.

  Aligns with the BIDS phenotype standard (https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files/phenotypic-and-assessment-data.html)
  and with NIDM''s ``nidm:Phenotype`` concept. Per-measure metadata can optionally
  carry Cognitive Atlas (https://www.cognitiveatlas.org/) ``cogat:Task`` and ``cogat:Concept``
  IRIs via ``measure_specs``.'
from_schema: https://w3id.org/tvbo
slots:
- label
- description
attributes:
  dataset_id:
    name: dataset_id
    description: Unique identifier for this phenotype bundle.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:identifier
    domain_of:
    - Dataset
    - Phenotype
    range: string
    required: true
  subjects:
    name: subjects
    description: Ordered list of subject IDs (e.g. HCP-YA 6-digit IDs). Each ``measures/<name>``
      array in the h5 companion is indexed by this order.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Dataset
    - Phenotype
    range: string
    required: true
    multivalued: true
  measures:
    name: measures
    description: 'Names of the measures present in the h5 companion (one ``measures/<name>``
      dataset per name). Example: ``[g_factor, PMAT24_A_CR, PMAT24_A_RTCR, CardSort_Unadj,
      ProcSpeed_Unadj]``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Phenotype
    range: string
    multivalued: true
  measure_specs:
    name: measure_specs
    description: Optional per-measure metadata (Cognitive Atlas IRIs, units, description).
      When present, each entry's ``name`` must match an entry in ``measures``.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Phenotype
    range: MeasureSpec
    multivalued: true
    inlined_as_list: true
  category:
    name: category
    description: 'Coarse classification of the phenotype bundle, used for filtering
      in larger study libraries. Canonical values: ``cognitive`` (intelligence / memory
      / attention scores), ``clinical`` (UPDRS, MMSE, …), ``behavioral`` (raw task
      outputs), ``demographic``, ``physiological``, ``derived`` (composite scores
      like g-factor or brain-age). Free string — extend as needed.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(cognitive)
    domain_of:
    - Phenotype
    range: string
  data_file:
    name: data_file
    description: Path to the h5 companion (relative to the yaml).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Phenotype
    - Network
    range: string
    required: true
  cohort:
    name: cohort
    description: Cohort label (e.g. 'HCPYA', 'PPMI').
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Phenotype
    - BidsEntities
    range: string
  provenance:
    name: provenance
    description: W3C PROV-O metadata for the source of these scores.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Phenotype
    - Network
    range: Provenance
    inlined: true
class_uri: tvbo:Phenotype

Induced

name: Phenotype
description: 'Per-subject phenotype table (BIDS ``phenotype/`` directory convention).
  Carries cognitive scores, clinical scales, demographic variables, behavioral task
  outputs, physiological measures, or any other per-subject numeric measurement bundle
  for a cohort. Sidecar companion to per-subject Network sidecars in multi-subject
  studies that correlate simulated quantities with empirical scores (e.g. PMAT24_A,
  g-factor, CardSort, ProcSpeed for Schirner 2023). The yaml carries metadata + the
  measure list; the h5 carries ``measures/<name>`` 1-D float arrays of length ``len(subjects)``.

  Aligns with the BIDS phenotype standard (https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files/phenotypic-and-assessment-data.html)
  and with NIDM''s ``nidm:Phenotype`` concept. Per-measure metadata can optionally
  carry Cognitive Atlas (https://www.cognitiveatlas.org/) ``cogat:Task`` and ``cogat:Concept``
  IRIs via ``measure_specs``.'
from_schema: https://w3id.org/tvbo
attributes:
  dataset_id:
    name: dataset_id
    description: Unique identifier for this phenotype bundle.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:identifier
    owner: Phenotype
    domain_of:
    - Dataset
    - Phenotype
    range: string
    required: true
  subjects:
    name: subjects
    description: Ordered list of subject IDs (e.g. HCP-YA 6-digit IDs). Each ``measures/<name>``
      array in the h5 companion is indexed by this order.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Dataset
    - Phenotype
    range: string
    required: true
    multivalued: true
  measures:
    name: measures
    description: 'Names of the measures present in the h5 companion (one ``measures/<name>``
      dataset per name). Example: ``[g_factor, PMAT24_A_CR, PMAT24_A_RTCR, CardSort_Unadj,
      ProcSpeed_Unadj]``.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Phenotype
    range: string
    multivalued: true
  measure_specs:
    name: measure_specs
    description: Optional per-measure metadata (Cognitive Atlas IRIs, units, description).
      When present, each entry's ``name`` must match an entry in ``measures``.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Phenotype
    range: MeasureSpec
    multivalued: true
    inlined: true
    inlined_as_list: true
  category:
    name: category
    description: 'Coarse classification of the phenotype bundle, used for filtering
      in larger study libraries. Canonical values: ``cognitive`` (intelligence / memory
      / attention scores), ``clinical`` (UPDRS, MMSE, …), ``behavioral`` (raw task
      outputs), ``demographic``, ``physiological``, ``derived`` (composite scores
      like g-factor or brain-age). Free string — extend as needed.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(cognitive)
    owner: Phenotype
    domain_of:
    - Phenotype
    range: string
  data_file:
    name: data_file
    description: Path to the h5 companion (relative to the yaml).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Phenotype
    - Network
    range: string
    required: true
  cohort:
    name: cohort
    description: Cohort label (e.g. 'HCPYA', 'PPMI').
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Phenotype
    - BidsEntities
    range: string
  provenance:
    name: provenance
    description: W3C PROV-O metadata for the source of these scores.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Phenotype
    domain_of:
    - Phenotype
    - Network
    range: Provenance
    inlined: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: Phenotype
    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: Phenotype
    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
class_uri: tvbo:Phenotype