Class: Network

Network specification with nodes, edges, and reusable coupling configurations. Supports both explicit node/edge representation and matrix-based connectivity (Connectome compatibility).

URI: tvbo:Network

 classDiagram
    class Network
    click Network href "./Network.html"
      Network : bids
        
          
    
        
        
        Network --> "0..1" BidsEntities : bids
        click BidsEntities href "./BidsEntities.html"
    

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

        
      Network : coordinate_space
        
          
    
        
        
        Network --> "0..1" CommonCoordinateSpace : coordinate_space
        click CommonCoordinateSpace href "./CommonCoordinateSpace.html"
    

        
      Network : coupling
        
          
    
        
        
        Network --> "*" Coupling : coupling
        click Coupling href "./Coupling.html"
    

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

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

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

        
      Network : distance_unit
        
          
    
        
        
        Network --> "0..1" UnitEnum : distance_unit
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Network : dynamics
        
          
    
        
        
        Network --> "*" Dynamics : dynamics
        click Dynamics href "./Dynamics.html"
    

        
      Network : edge_matrix_files
        
          
    
        
        
        Network --> "*" File : edge_matrix_files
        click File href "./File.html"
    

        
      Network : edges
        
          
    
        
        
        Network --> "*" Edge : edges
        click Edge href "./Edge.html"
    

        
      Network : graph_generator
        
          
    
        
        
        Network --> "0..1" GraphGenerator : graph_generator
        click GraphGenerator href "./GraphGenerator.html"
    

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

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

        
      Network : nodes
        
          
    
        
        
        Network --> "*" Node : nodes
        click Node href "./Node.html"
    

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

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

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

        
      Network : parcellation
        
          
    
        
        
        Network --> "0..1" Parcellation : parcellation
        click Parcellation href "./Parcellation.html"
    

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

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

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

        
      Network : time_unit
        
          
    
        
        
        Network --> "0..1" UnitEnum : time_unit
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Network : tractogram
        
          
    
        
        
        Network --> "0..1" Tractogram : tractogram
        click Tractogram href "./Tractogram.html"
    

        
      Network : transforms
        
          
    
        
        
        Network --> "*" Function : transforms
        click Function href "./Function.html"

Class Properties

Property Value
Class URI tvbo:Network

Slots

Name Cardinality and Range Description Inheritance
label 0..1
xsd:string		 direct
description 0..1
xsd:string		 direct
parameters *
Parameter		 direct
nodes *
Node		 List of nodes with individual dynamics (optional, for heterogeneous networks) direct
edges *
Edge		 List of directed edges with coupling references (optional, for explicit edge … direct
coupling *
Coupling		 Reusable coupling configurations referenced by edges (e direct
dynamics *
Dynamics		 Dictionary of dynamics models keyed by name direct
number_of_nodes 0..1
xsd:integer		 Number of nodes in the network (derived from nodes if not set) direct
coordinate_space 0..1
CommonCoordinateSpace		 Coordinate space for node positions (e direct
parcellation 0..1
Parcellation		 Brain parcellation/atlas reference direct
tractogram 0..1
Tractogram		 Reference to tractography data direct
transforms *
Function		 Ordered list of transforms applied to edge property matrices direct
data_file 0..1
xsd:string		 Path to companion data file direct
descriptor 0..1
xsd:string		 Short alphanumeric identifier for the BIDS desc- filename entity (e direct
bids_dir 0..1
xsd:string		 Path to BEP017-compliant BIDS directory for loading connectivity matrices direct
bids 0..1
BidsEntities		 BIDS filename entities for this dataset direct
structural_measures *
xsd:string		 BEP017 measure names for structural connectivity (e direct
observational_measures *
xsd:string		 BEP017 measure names for observational targets (e direct
provenance 0..1
Provenance		 W3C PROV-O aligned provenance direct
parent_network 0..1
xsd:string		 Path/URI to parent (coarser) Network direct
node_mapping 0..1
xsd:string		 HDF5 dataset path for node-to-parent mapping direct
distance_unit 0..1
UnitEnum		 Unit for distances/lengths in the network direct
time_unit 0..1
UnitEnum		 Default time unit for the network direct
edge_matrix_files *
File		 direct
graph_generator 0..1
GraphGenerator		 Graph generator specification direct

Usages

used by used in type used
Coupling regional_connectivity range Network
SimulationExperiment connectivity range Network
SimulationExperiment network range Network

Aliases

  • Network
  • Connectome
  • Graph
  • Connectivity

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Network
description: Network specification with nodes, edges, and reusable coupling configurations.
  Supports both explicit node/edge representation and matrix-based connectivity (Connectome
  compatibility).
from_schema: https://w3id.org/tvbo
aliases:
- Network
- Connectome
- Graph
- Connectivity
slots:
- label
- description
- parameters
attributes:
  nodes:
    name: nodes
    description: List of nodes with individual dynamics (optional, for heterogeneous
      networks)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Node
    multivalued: true
    inlined: true
    inlined_as_list: true
  edges:
    name: edges
    description: List of directed edges with coupling references (optional, for explicit
      edge definition)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Edge
    multivalued: true
    inlined: true
    inlined_as_list: true
  coupling:
    name: coupling
    description: Reusable coupling configurations referenced by edges (e.g., 'instant',
      'delayed', 'inhibitory')
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    - Edge
    - SimulationExperiment
    range: Coupling
    multivalued: true
    inlined: true
  dynamics:
    name: dynamics
    description: Dictionary of dynamics models keyed by name. Nodes reference these
      by name. For heterogeneous networks with per-node dynamics.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    multivalued: true
    inlined: true
  number_of_nodes:
    name: number_of_nodes
    description: Number of nodes in the network (derived from nodes if not set)
    from_schema: https://w3id.org/tvbo
    aliases:
    - number_of_nodes
    - number_of_regions
    rank: 1000
    ifabsent: integer(1)
    domain_of:
    - Network
    range: integer
  coordinate_space:
    name: coordinate_space
    description: Coordinate space for node positions (e.g., MNI152NLin2009c). Mirrors
      BrainAtlas.coordinateSpace so network node positions are unambiguous.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Dataset
    - Subject
    - Electrode
    - EField
    - Network
    - SpatialDomain
    - Mesh
    range: CommonCoordinateSpace
    inlined: true
  parcellation:
    name: parcellation
    description: Brain parcellation/atlas reference
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Parcellation
    inlined: true
  tractogram:
    name: tractogram
    description: Reference to tractography data
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Tractogram
    inlined: true
  transforms:
    name: transforms
    description: Ordered list of transforms applied to edge property matrices. Each
      Function's name identifies the target edge property (e.g. 'weight', 'length').
      Supports equation-based (symbolic) or callable-based (software) transforms.
      Multiple transforms on the same target are applied sequentially.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Function
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_file:
    name: data_file
    description: 'Path to companion data file. Supported extensions: .h5 (HDF5), .zarr/
      (Zarr), .csv (legacy single-matrix). Null if no companion data needed.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
  descriptor:
    name: descriptor
    description: Short alphanumeric identifier for the BIDS desc- filename entity
      (e.g., SC, FC, EC, SCFC). Classifies the connectivity modality of the network's
      edge measures.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
  bids_dir:
    name: bids_dir
    description: Path to BEP017-compliant BIDS directory for loading connectivity
      matrices
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
  bids:
    name: bids
    description: BIDS filename entities for this dataset
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: BidsEntities
    inlined: true
  structural_measures:
    name: structural_measures
    description: BEP017 measure names for structural connectivity (e.g., streamlineCount,
      tractLength)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
    multivalued: true
  observational_measures:
    name: observational_measures
    description: BEP017 measure names for observational targets (e.g., BoldCorrelation)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
    multivalued: true
  provenance:
    name: provenance
    description: W3C PROV-O aligned provenance
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: Provenance
    inlined: true
  parent_network:
    name: parent_network
    description: Path/URI to parent (coarser) Network. When set, this network is a
      refinement where each node maps to exactly one parent node via node_mapping.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
  node_mapping:
    name: node_mapping
    description: HDF5 dataset path for node-to-parent mapping. Int32 array of shape
      (N,) where entry i is the parent node ID. Required when parent_network is set.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: string
  distance_unit:
    name: distance_unit
    description: Unit for distances/lengths in the network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(mm)
    domain_of:
    - Network
    range: UnitEnum
  time_unit:
    name: time_unit
    description: Default time unit for the network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(ms)
    domain_of:
    - Network
    range: UnitEnum
  edge_matrix_files:
    name: edge_matrix_files
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: File
    multivalued: true
  graph_generator:
    name: graph_generator
    description: 'Graph generator specification.  When set, overrides explicit edges/nodes
      for graph construction.  The type field is a free string; StandardGraphType
      lists well-known types that get automatic code generation across backends.

      '
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Network
    range: GraphGenerator
    inlined: true
class_uri: tvbo:Network

Induced

name: Network
description: Network specification with nodes, edges, and reusable coupling configurations.
  Supports both explicit node/edge representation and matrix-based connectivity (Connectome
  compatibility).
from_schema: https://w3id.org/tvbo
aliases:
- Network
- Connectome
- Graph
- Connectivity
attributes:
  nodes:
    name: nodes
    description: List of nodes with individual dynamics (optional, for heterogeneous
      networks)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: nodes
    owner: Network
    domain_of:
    - Network
    range: Node
    multivalued: true
    inlined: true
    inlined_as_list: true
  edges:
    name: edges
    description: List of directed edges with coupling references (optional, for explicit
      edge definition)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: edges
    owner: Network
    domain_of:
    - Network
    range: Edge
    multivalued: true
    inlined: true
    inlined_as_list: true
  coupling:
    name: coupling
    description: Reusable coupling configurations referenced by edges (e.g., 'instant',
      'delayed', 'inhibitory')
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: coupling
    owner: Network
    domain_of:
    - Network
    - Edge
    - SimulationExperiment
    range: Coupling
    multivalued: true
    inlined: true
  dynamics:
    name: dynamics
    description: Dictionary of dynamics models keyed by name. Nodes reference these
      by name. For heterogeneous networks with per-node dynamics.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: dynamics
    owner: Network
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    multivalued: true
    inlined: true
  number_of_nodes:
    name: number_of_nodes
    description: Number of nodes in the network (derived from nodes if not set)
    from_schema: https://w3id.org/tvbo
    aliases:
    - number_of_nodes
    - number_of_regions
    rank: 1000
    ifabsent: integer(1)
    alias: number_of_nodes
    owner: Network
    domain_of:
    - Network
    range: integer
  coordinate_space:
    name: coordinate_space
    description: Coordinate space for node positions (e.g., MNI152NLin2009c). Mirrors
      BrainAtlas.coordinateSpace so network node positions are unambiguous.
    from_schema: https://w3id.org/tvbo
    alias: coordinate_space
    owner: Network
    domain_of:
    - Dataset
    - Subject
    - Electrode
    - EField
    - Network
    - SpatialDomain
    - Mesh
    range: CommonCoordinateSpace
    inlined: true
  parcellation:
    name: parcellation
    description: Brain parcellation/atlas reference
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: parcellation
    owner: Network
    domain_of:
    - Network
    range: Parcellation
    inlined: true
  tractogram:
    name: tractogram
    description: Reference to tractography data
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: tractogram
    owner: Network
    domain_of:
    - Network
    range: Tractogram
    inlined: true
  transforms:
    name: transforms
    description: Ordered list of transforms applied to edge property matrices. Each
      Function's name identifies the target edge property (e.g. 'weight', 'length').
      Supports equation-based (symbolic) or callable-based (software) transforms.
      Multiple transforms on the same target are applied sequentially.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: transforms
    owner: Network
    domain_of:
    - Network
    range: Function
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_file:
    name: data_file
    description: 'Path to companion data file. Supported extensions: .h5 (HDF5), .zarr/
      (Zarr), .csv (legacy single-matrix). Null if no companion data needed.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: data_file
    owner: Network
    domain_of:
    - Network
    range: string
  descriptor:
    name: descriptor
    description: Short alphanumeric identifier for the BIDS desc- filename entity
      (e.g., SC, FC, EC, SCFC). Classifies the connectivity modality of the network's
      edge measures.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: descriptor
    owner: Network
    domain_of:
    - Network
    range: string
  bids_dir:
    name: bids_dir
    description: Path to BEP017-compliant BIDS directory for loading connectivity
      matrices
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: bids_dir
    owner: Network
    domain_of:
    - Network
    range: string
  bids:
    name: bids
    description: BIDS filename entities for this dataset
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: bids
    owner: Network
    domain_of:
    - Network
    range: BidsEntities
    inlined: true
  structural_measures:
    name: structural_measures
    description: BEP017 measure names for structural connectivity (e.g., streamlineCount,
      tractLength)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: structural_measures
    owner: Network
    domain_of:
    - Network
    range: string
    multivalued: true
  observational_measures:
    name: observational_measures
    description: BEP017 measure names for observational targets (e.g., BoldCorrelation)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: observational_measures
    owner: Network
    domain_of:
    - Network
    range: string
    multivalued: true
  provenance:
    name: provenance
    description: W3C PROV-O aligned provenance
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: provenance
    owner: Network
    domain_of:
    - Network
    range: Provenance
    inlined: true
  parent_network:
    name: parent_network
    description: Path/URI to parent (coarser) Network. When set, this network is a
      refinement where each node maps to exactly one parent node via node_mapping.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: parent_network
    owner: Network
    domain_of:
    - Network
    range: string
  node_mapping:
    name: node_mapping
    description: HDF5 dataset path for node-to-parent mapping. Int32 array of shape
      (N,) where entry i is the parent node ID. Required when parent_network is set.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: node_mapping
    owner: Network
    domain_of:
    - Network
    range: string
  distance_unit:
    name: distance_unit
    description: Unit for distances/lengths in the network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(mm)
    alias: distance_unit
    owner: Network
    domain_of:
    - Network
    range: UnitEnum
  time_unit:
    name: time_unit
    description: Default time unit for the network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(ms)
    alias: time_unit
    owner: Network
    domain_of:
    - Network
    range: UnitEnum
  edge_matrix_files:
    name: edge_matrix_files
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: edge_matrix_files
    owner: Network
    domain_of:
    - Network
    range: File
    multivalued: true
  graph_generator:
    name: graph_generator
    description: 'Graph generator specification.  When set, overrides explicit edges/nodes
      for graph construction.  The type field is a free string; StandardGraphType
      lists well-known types that get automatic code generation across backends.

      '
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: graph_generator
    owner: Network
    domain_of:
    - Network
    range: GraphGenerator
    inlined: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: Network
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Continuation
    - 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: Network
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - Network
    - GraphGenerator
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: parameters
    owner: Network
    domain_of:
    - Equation
    - Stimulus
    - Event
    - TemporalApplicableEquation
    - Network
    - GraphGenerator
    - Node
    - Edge
    - Observation
    - Dynamics
    - Distribution
    - Noise
    - Exploration
    - Discretization
    - BranchSwitch
    - Integrator
    - Coupling
    - PDE
    range: Parameter
    multivalued: true
    inlined: true
class_uri: tvbo:Network