Reference·Classes

Class: DataRef

A pointer to one labelled array in a result container, dataset, or curated entity — the single cross-container reference primitive (a PROV entity a consumer prov:used). WHERE is experiment (an in-study experiment id, resolved like initial_state.source_experiment), analysis (an in-study analysis name), or the full iri (a curated / result / external pointer); at most one. WHICH is output (a recorded variable, observation__<name>, estimate__<param>, or external variable). SLICE is sel (label-keyed .sel, never positional). reconcile optionally aligns the sourced array to the consuming network’s node order by label. One model reused by figure layers (Layer.used), sourced arguments (Argument.used) and sourced parameters (Parameter.used), so data binding, cross-experiment sourcing and PROV provenance are the same edge. A sourced array is resolved lazily and never inlined into generated code.

URI: prov:Entity

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

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

        
      DataRef : iri
        
          
    
        
        
        DataRef --> "0..1" Uriorcurie : iri
        click Uriorcurie href "../http://www.w3.org/2001/XMLSchema#anyURI.html"
    

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

        
      DataRef : reconcile
        
          
    
        
        
        DataRef --> "0..1" NodeReconciliation : reconcile
        click NodeReconciliation href "../../enums/NodeReconciliation.html"
    

        
      DataRef : sel
        
          
    
        
        
        DataRef --> "*" Argument : sel
        click Argument href "./Argument.html"
    

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

        
      

Class Properties

Property	Value
Class URI	prov:Entity

Slots

Name	Cardinality and Range	Description	Inheritance
iri	0..1 xsd:anyURI	Optional stable IRI (or compact URI) for this entity in an external ontology …	direct
experiment	0..1 xsd:string or  xsd:integer	WHERE (short form): an in-study experiment id whose saved result holds the ar…	direct
analysis	0..1 xsd:string	WHERE (short form): an in-study analysis name whose saved result holds the ar…	direct
output	0..1 xsd:string	WHICH array to take from the container at experiment / iri: a recorde…	direct
sel	* Argument	SLICE: label-based selector (xarray | direct | | [transform](../slots/transform.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Optional named reduction applied to the sourced array aftersel, before `... | direct | | [reconcile](../slots/reconcile.qmd) | 0..1 <br/> [NodeReconciliation](../enums/NodeReconciliation.qmd) | Align the sourced array's nodes to the consuming network by label (by_label…	direct

Usages

used by	used in	type	used
Layer	used	range	DataRef
Annotation	used	range	DataRef
Annotation	tail_used	range	DataRef
Parameter	used	range	DataRef
Argument	used	range	DataRef
DerivedParameter	used	range	DataRef
ResultBinding	used	range	DataRef

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	prov:Entity
native	tvbo:DataRef

LinkML Source

Direct

name: DataRef
description: A pointer to one labelled array in a result container, dataset, or curated
  entity — the single cross-container reference primitive (a PROV entity a consumer
  ``prov:used``). WHERE is ``experiment`` (an in-study experiment id, resolved like
  ``initial_state.source_experiment``), ``analysis`` (an in-study analysis name),
  or the full ``iri`` (a curated / result / external pointer); at most one. WHICH
  is ``output`` (a recorded variable, ``observation__<name>``, ``estimate__<param>``,
  or external variable). SLICE is ``sel`` (label-keyed ``.sel``, never positional).
  ``reconcile`` optionally aligns the sourced array to the consuming network's node
  order by label. One model reused by figure layers (``Layer.used``), sourced arguments
  (``Argument.used``) and sourced parameters (``Parameter.used``), so data binding,
  cross-experiment sourcing and PROV provenance are the same edge. A sourced array
  is resolved lazily and never inlined into generated code.
from_schema: https://w3id.org/tvbo/common
slots:
- iri
attributes:
  experiment:
    name: experiment
    description: 'WHERE (short form): an in-study experiment id whose saved result
      holds the array, resolved within the enclosing study like ``initial_state.source_experiment``.
      Written as the bare integer id (``34``), or as one of the string spellings the
      workflow planner also accepts (``exp-34``, ``"34"``) — ``tvbo.data.dataref``
      normalises all three to the integer it globs the container by. Mutually exclusive
      with ``iri`` (the full cross-study / curated / external form). When both are
      absent the reference is local — ``output`` names this experiment''s own output
      — otherwise falling back to ``initial_state.source_experiment`` when present.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    domain_of:
    - DataRef
    any_of:
    - range: integer
    - range: string
  analysis:
    name: analysis
    description: 'WHERE (short form): an in-study analysis name whose saved result
      holds the array (``derivatives/tvbo/ana-<name>_result.h5``). Mutually exclusive
      with ``experiment`` and ``iri``, and — like ``experiment`` — it registers the
      run-order dependency, so the analysis runs before whatever consumes it.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    domain_of:
    - DataRef
    - Observation
    range: string
  output:
    name: output
    description: 'WHICH array to take from the container at ``experiment`` / ``iri``:
      a recorded state variable, an ``observation__<name>``, an ``estimate__<param>``
      (a tuned free parameter a fit persisted), or an external variable. Matched exactly
      or by the ``<producer>__<name>`` suffix.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    domain_of:
    - DataRef
    - Procedure
    - Dynamics
    - Function
    - FunctionCall
    range: string
  sel:
    name: sel
    description: 'SLICE: label-based selector (xarray ``.sel``), keyed by dimension
      (reuses ``Argument``; name = dim, value = coordinate label), taking the nearest
      coordinate for a numeric selection. Never positional — picks e.g. one operating
      point out of a swept branch by its parameter value.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    domain_of:
    - DataRef
    range: Argument
    multivalued: true
    inlined: true
  transform:
    name: transform
    description: Optional named reduction applied to the sourced array after ``sel``,
      before ``reconcile`` — a registered ``fn(da) -> da`` (the same ``bsplot.register_transform``
      registry a figure ``Layer.transform`` uses). Handles a selection a label ``sel``
      cannot express on its own, e.g. picking the operating point (endpoint) out of
      a branch-restart container keyed by ordinal. Presentation/selection only — prefer
      a ``sel`` or an upstream observation when one suffices.
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    domain_of:
    - DataRef
    - Layer
    - ExplorationAxis
    range: string
  reconcile:
    name: reconcile
    description: Align the sourced array's nodes to the consuming network by label
      (``by_label``) or take it as-is (``none``, the default — a sibling experiment
      usually already shares the node order). A property of the reference, so figure
      layers, dataset targets and warm-starts share one flag.
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    ifabsent: none
    domain_of:
    - DataRef
    - Observation
    range: NodeReconciliation
class_uri: prov:Entity

Induced

name: DataRef
description: A pointer to one labelled array in a result container, dataset, or curated
  entity — the single cross-container reference primitive (a PROV entity a consumer
  ``prov:used``). WHERE is ``experiment`` (an in-study experiment id, resolved like
  ``initial_state.source_experiment``), ``analysis`` (an in-study analysis name),
  or the full ``iri`` (a curated / result / external pointer); at most one. WHICH
  is ``output`` (a recorded variable, ``observation__<name>``, ``estimate__<param>``,
  or external variable). SLICE is ``sel`` (label-keyed ``.sel``, never positional).
  ``reconcile`` optionally aligns the sourced array to the consuming network's node
  order by label. One model reused by figure layers (``Layer.used``), sourced arguments
  (``Argument.used``) and sourced parameters (``Parameter.used``), so data binding,
  cross-experiment sourcing and PROV provenance are the same edge. A sourced array
  is resolved lazily and never inlined into generated code.
from_schema: https://w3id.org/tvbo/common
attributes:
  experiment:
    name: experiment
    description: 'WHERE (short form): an in-study experiment id whose saved result
      holds the array, resolved within the enclosing study like ``initial_state.source_experiment``.
      Written as the bare integer id (``34``), or as one of the string spellings the
      workflow planner also accepts (``exp-34``, ``"34"``) — ``tvbo.data.dataref``
      normalises all three to the integer it globs the container by. Mutually exclusive
      with ``iri`` (the full cross-study / curated / external form). When both are
      absent the reference is local — ``output`` names this experiment''s own output
      — otherwise falling back to ``initial_state.source_experiment`` when present.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    owner: DataRef
    domain_of:
    - DataRef
    range: string
    any_of:
    - range: integer
    - range: string
  analysis:
    name: analysis
    description: 'WHERE (short form): an in-study analysis name whose saved result
      holds the array (``derivatives/tvbo/ana-<name>_result.h5``). Mutually exclusive
      with ``experiment`` and ``iri``, and — like ``experiment`` — it registers the
      run-order dependency, so the analysis runs before whatever consumes it.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    owner: DataRef
    domain_of:
    - DataRef
    - Observation
    range: string
  output:
    name: output
    description: 'WHICH array to take from the container at ``experiment`` / ``iri``:
      a recorded state variable, an ``observation__<name>``, an ``estimate__<param>``
      (a tuned free parameter a fit persisted), or an external variable. Matched exactly
      or by the ``<producer>__<name>`` suffix.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    owner: DataRef
    domain_of:
    - DataRef
    - Procedure
    - Dynamics
    - Function
    - FunctionCall
    range: string
  sel:
    name: sel
    description: 'SLICE: label-based selector (xarray ``.sel``), keyed by dimension
      (reuses ``Argument``; name = dim, value = coordinate label), taking the nearest
      coordinate for a numeric selection. Never positional — picks e.g. one operating
      point out of a swept branch by its parameter value.'
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    owner: DataRef
    domain_of:
    - DataRef
    range: Argument
    multivalued: true
    inlined: true
  transform:
    name: transform
    description: Optional named reduction applied to the sourced array after ``sel``,
      before ``reconcile`` — a registered ``fn(da) -> da`` (the same ``bsplot.register_transform``
      registry a figure ``Layer.transform`` uses). Handles a selection a label ``sel``
      cannot express on its own, e.g. picking the operating point (endpoint) out of
      a branch-restart container keyed by ordinal. Presentation/selection only — prefer
      a ``sel`` or an upstream observation when one suffices.
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    owner: DataRef
    domain_of:
    - DataRef
    - Layer
    - ExplorationAxis
    range: string
  reconcile:
    name: reconcile
    description: Align the sourced array's nodes to the consuming network by label
      (``by_label``) or take it as-is (``none``, the default — a sibling experiment
      usually already shares the node order). A property of the reference, so figure
      layers, dataset targets and warm-starts share one flag.
    from_schema: https://w3id.org/tvbo/common
    rank: 1000
    ifabsent: none
    owner: DataRef
    domain_of:
    - DataRef
    - Observation
    range: NodeReconciliation
  iri:
    name: iri
    description: Optional stable IRI (or compact URI) for this entity in an external
      ontology or knowledge base. Used to load metadata from an external source; not
      required when the entity is fully self-contained (equations, parameters, etc.
      defined in the file itself).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:identifier
    owner: DataRef
    domain_of:
    - DataRef
    - Theme
    - Parcellation
    - Tractogram
    - ResultEntity
    - Activity
    - ReferenceFingerprint
    - GraphGenerator
    - Reference
    - Observation
    - Dynamics
    - Function
    - FunctionCall
    - Coupling
    range: uriorcurie
class_uri: prov:Entity