Class: StudyLayout

Directory layout of a study dataset, and the single ground truth for it. Everything that creates, resolves, ignores, validates or documents a study’s directories reads this record instead of restating the tree, so the layout cannot drift between the scaffolder, the path resolvers, the ignore files, the validator and the docs. The vocabulary deliberately mirrors the BIDS rules/directories.yaml (name, level, opaque, subdirs) so a layout can be diffed against the standard.

URI: tvbo_study:class/StudyLayout

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

        
      StudyLayout : dataset_type
        
          
    
        
        
        StudyLayout --> "0..1" BidsDatasetType : dataset_type
        click BidsDatasetType href "../../enums/BidsDatasetType.html"
    

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

        
      StudyLayout : files
        
          
    
        
        
        StudyLayout --> "*" StudyFile : files
        click StudyFile href "./StudyFile.html"
    

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

        
      StudyLayout : subdirs
        
          
    
        
        
        StudyLayout --> "*" StudyDirectory : subdirs
        click StudyDirectory href "./StudyDirectory.html"
    

        
      StudyLayout : templates
        
          
    
        
        
        StudyLayout --> "*" StudyTemplate : templates
        click StudyTemplate href "./StudyTemplate.html"

Slots

Name Cardinality and Range Description Inheritance
name 1
xsd:string		 Globally unique identifier for the entity direct
description 0..1
xsd:string		 direct
dataset_type 0..1
BidsDatasetType		 BIDS DatasetType this layout realises, written into the dataset’s datas... | direct | | [bids_version](../slots/bids_version.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | BIDS version the layout was written against | direct | | [subdirs](../slots/subdirs.qmd) | * <br/> [StudyDirectory](../classes/StudyDirectory.qmd) | Directories under the dataset root, in the order a reader should meet them | direct | | [files](../slots/files.qmd) | * <br/> [StudyFile](../classes/StudyFile.qmd) | Files at the dataset root | direct | | [templates](../slots/templates.qmd) | * <br/> [StudyTemplate](../classes/StudyTemplate.qmd) | The kinds of study this record covers, keyed by the nametvbo study init –… direct

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self tvbo_study:StudyLayout
native tvbo_study:StudyLayout

LinkML Source

Direct

name: StudyLayout
description: Directory layout of a study dataset, and the single ground truth for
  it. Everything that creates, resolves, ignores, validates or documents a study's
  directories reads this record instead of restating the tree, so the layout cannot
  drift between the scaffolder, the path resolvers, the ignore files, the validator
  and the docs. The vocabulary deliberately mirrors the BIDS ``rules/directories.yaml``
  (``name``, ``level``, ``opaque``, ``subdirs``) so a layout can be diffed against
  the standard.
from_schema: https://w3id.org/tvbo/study
slots:
- name
- description
attributes:
  dataset_type:
    name: dataset_type
    description: BIDS ``DatasetType`` this layout realises, written into the dataset's
      ``dataset_description.json``.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    ifabsent: string(study)
    domain_of:
    - StudyLayout
    range: BidsDatasetType
  bids_version:
    name: bids_version
    description: BIDS version the layout was written against.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyLayout
    range: string
  subdirs:
    name: subdirs
    description: Directories under the dataset root, in the order a reader should
      meet them.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyLayout
    - StudyDirectory
    range: StudyDirectory
    multivalued: true
    inlined: true
    inlined_as_list: true
  files:
    name: files
    description: Files at the dataset root.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyLayout
    - StudyDirectory
    range: StudyFile
    multivalued: true
    inlined: true
    inlined_as_list: true
  templates:
    name: templates
    description: The kinds of study this record covers, keyed by the name ``tvbo study
      init --template`` takes. An entry's ``in_templates`` names one of these, so
      a template that nothing declares is a typo rather than a silently empty variant.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyLayout
    range: StudyTemplate
    multivalued: true
    inlined: true

Induced

name: StudyLayout
description: Directory layout of a study dataset, and the single ground truth for
  it. Everything that creates, resolves, ignores, validates or documents a study's
  directories reads this record instead of restating the tree, so the layout cannot
  drift between the scaffolder, the path resolvers, the ignore files, the validator
  and the docs. The vocabulary deliberately mirrors the BIDS ``rules/directories.yaml``
  (``name``, ``level``, ``opaque``, ``subdirs``) so a layout can be diffed against
  the standard.
from_schema: https://w3id.org/tvbo/study
attributes:
  dataset_type:
    name: dataset_type
    description: BIDS ``DatasetType`` this layout realises, written into the dataset's
      ``dataset_description.json``.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    ifabsent: string(study)
    owner: StudyLayout
    domain_of:
    - StudyLayout
    range: BidsDatasetType
  bids_version:
    name: bids_version
    description: BIDS version the layout was written against.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyLayout
    domain_of:
    - StudyLayout
    range: string
  subdirs:
    name: subdirs
    description: Directories under the dataset root, in the order a reader should
      meet them.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyLayout
    domain_of:
    - StudyLayout
    - StudyDirectory
    range: StudyDirectory
    multivalued: true
    inlined: true
    inlined_as_list: true
  files:
    name: files
    description: Files at the dataset root.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyLayout
    domain_of:
    - StudyLayout
    - StudyDirectory
    range: StudyFile
    multivalued: true
    inlined: true
    inlined_as_list: true
  templates:
    name: templates
    description: The kinds of study this record covers, keyed by the name ``tvbo study
      init --template`` takes. An entry's ``in_templates`` names one of these, so
      a template that nothing declares is a typo rather than a silently empty variant.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyLayout
    domain_of:
    - StudyLayout
    range: StudyTemplate
    multivalued: true
    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: StudyLayout
    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
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: StudyLayout
    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