# Class: StudyCollection 


_The whole manuscript as one runnable specification: a study that aggregates the member studies a paper reports (``members``) and also owns the paper's own demonstration experiments, analyses and figures (the SimulationStudy slots it inherits). ``tvbo run`` walks the members and the owned content, emits every reported number to a results manifest (``results``) and every figure with its composed caption, then packages the lot as a COMBINE/OMEX archive (``archive``) — so the paper becomes an instance of the reproducibility it argues for. A Study-of-studies, which no SimulationStudy is (``experiments`` ranges over experiments, not studies); legitimized by COMBINE/OMEX, SED-ML and the ISA ``Investigation`` top-level container it parallels._



<div data-search-exclude markdown="1">



URI: [tvbo:StudyCollection](https://w3id.org/tvbo/StudyCollection)





```{mermaid}
 classDiagram
    class StudyCollection
    click StudyCollection href "./StudyCollection.html"
      SimulationStudy <|-- StudyCollection
        click SimulationStudy href "./SimulationStudy.html"
      
      StudyCollection : analyses
        
          
    
        
        
        StudyCollection --> "*" Analysis : analyses
        click Analysis href "./Analysis.html"
    

        
      StudyCollection : archive
        
          
    
        
        
        StudyCollection --> "0..1" ArchiveConfig : archive
        click ArchiveConfig href "./ArchiveConfig.html"
    

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

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

        
      StudyCollection : code_source
        
          
    
        
        
        StudyCollection --> "0..1" CodeSource : code_source
        click CodeSource href "./CodeSource.html"
    

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

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

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

        
      StudyCollection : figures
        
          
    
        
        
        StudyCollection --> "*" Figure : figures
        click Figure href "./Figure.html"
    

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

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

        
      StudyCollection : members
        
          
    
        
        
        StudyCollection --> "*" StudyMember : members
        click StudyMember href "./StudyMember.html"
    

        
      StudyCollection : model
        
          
    
        
        
        StudyCollection --> "0..1" Dynamics : model
        click Dynamics href "./Dynamics.html"
    

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

        
      StudyCollection : results
        
          
    
        
        
        StudyCollection --> "*" ResultBinding : results
        click ResultBinding href "./ResultBinding.html"
    

        
      StudyCollection : sample
        
          
    
        
        
        StudyCollection --> "0..1" Sample : sample
        click Sample href "./Sample.html"
    

        
      StudyCollection : simulation_experiments
        
          
    
        
        
        StudyCollection --> "*" SimulationExperiment : simulation_experiments
        click SimulationExperiment href "./SimulationExperiment.html"
    

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

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

        
      StudyCollection : workflow
        
          
    
        
        
        StudyCollection --> "0..1" WorkflowConfig : workflow
        click WorkflowConfig href "./WorkflowConfig.html"
    

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

        
      
```





## Inheritance
* [Study](../classes/Study.qmd)
    * [SimulationStudy](../classes/SimulationStudy.qmd)
        * **StudyCollection**


## Class Properties

| Property | Value |
| --- | --- |
| Class URI | [tvbo:StudyCollection](https://w3id.org/tvbo/StudyCollection) |


## Slots

| Name | Cardinality and Range | Description | Inheritance |
| ---  | --- | --- | --- |
| [members](../slots/members.qmd) | * <br/> [StudyMember](../classes/StudyMember.qmd) | The member studies this collection aggregates, each a reference to a study re... | direct |
| [results](../slots/results.qmd) | * <br/> [ResultBinding](../classes/ResultBinding.qmd) | The named numbers the prose cites, each keyed by the manuscript token that st... | direct |
| [archive](../slots/archive.qmd) | 0..1 <br/> [ArchiveConfig](../classes/ArchiveConfig.qmd) | How to package the run into a COMBINE/OMEX archive — the single supplementary... | direct |
| [label](../slots/label.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [derived_from](../slots/derived_from.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [model](../slots/model.qmd) | 0..1 <br/> [Dynamics](../classes/Dynamics.qmd) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [references](../slots/references.qmd) | * <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [key](../slots/key.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Deprecated alias of the inherited ``citekey``; retained for back-compatibilit... | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [sample](../slots/sample.qmd) | 0..1 <br/> [Sample](../classes/Sample.qmd) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [workflow](../slots/workflow.qmd) | 0..1 <br/> [WorkflowConfig](../classes/WorkflowConfig.qmd) | Study-wide default orchestration for rendering its experiments' sweeps into d... | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [simulation_experiments](../slots/simulation_experiments.qmd) | * <br/> [SimulationExperiment](../classes/SimulationExperiment.qmd) |  | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [analyses](../slots/analyses.qmd) | * <br/> [Analysis](../classes/Analysis.qmd) | Analyses of this study's results, each persisted as its own container and so ... | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [figures](../slots/figures.qmd) | * <br/> [Figure](../classes/Figure.qmd) | Declarative Figure specs rendered from this study's experiment results — clos... | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [code_source](../slots/code_source.qmd) | 0..1 <br/> [CodeSource](../classes/CodeSource.qmd) | Where this study's callable code lives — the builders and transform/observati... | [SimulationStudy](../classes/SimulationStudy.qmd) |
| [description](../slots/description.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [Study](../classes/Study.qmd) |
| [citekey](../slots/citekey.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | BibTeX citation key; the join key into references | [Study](../classes/Study.qmd) |
| [type](../slots/type.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Publication type (article, book, inproceedings, …) | [Study](../classes/Study.qmd) |
| [title](../slots/title.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [Study](../classes/Study.qmd) |
| [authors](../slots/authors.qmd) | * <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Author display strings (full detail in references | [Study](../classes/Study.qmd) |
| [year](../slots/year.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) |  | [Study](../classes/Study.qmd) |
| [doi](../slots/doi.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | [Study](../classes/Study.qmd) |















## Identifier and Mapping Information





### Schema Source


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




## Mappings

| Mapping Type | Mapped Value |
| ---  | ---  |
| self | tvbo:StudyCollection |
| native | tvbo:StudyCollection |






## LinkML Source

<!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->

### Direct

<details>
```yaml
name: StudyCollection
description: 'The whole manuscript as one runnable specification: a study that aggregates
  the member studies a paper reports (``members``) and also owns the paper''s own
  demonstration experiments, analyses and figures (the SimulationStudy slots it inherits).
  ``tvbo run`` walks the members and the owned content, emits every reported number
  to a results manifest (``results``) and every figure with its composed caption,
  then packages the lot as a COMBINE/OMEX archive (``archive``) — so the paper becomes
  an instance of the reproducibility it argues for. A Study-of-studies, which no SimulationStudy
  is (``experiments`` ranges over experiments, not studies); legitimized by COMBINE/OMEX,
  SED-ML and the ISA ``Investigation`` top-level container it parallels.'
from_schema: https://w3id.org/tvbo
is_a: SimulationStudy
attributes:
  members:
    name: members
    description: The member studies this collection aggregates, each a reference to
      a study recipe (``recipe``) plus whether it is ``optional`` (skipped unless
      requested, for runs too heavy to recompute per build). ``tvbo run`` executes
      each member's own experiments, analyses and figures; the ``figures``/``analyses``
      inherited here are instead the paper-native demos that belong to no member.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StudyCollection
    range: StudyMember
    multivalued: true
    inlined: true
    inlined_as_list: true
  results:
    name: results
    description: The named numbers the prose cites, each keyed by the manuscript token
      that stands in for it (``key``) and bound either to a computed value (``used:``
      a DataRef into a member's or its own analysis) or to an authored constant quoted
      from prior work (``value`` + ``source``). ``tvbo run`` collects these into a
      results manifest the document reads, so no reported figure is transcribed by
      hand and a stale or missing key fails the build rather than printing a wrong
      number.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StudyCollection
    range: ResultBinding
    multivalued: true
    inlined: true
    inlined_as_list: true
  archive:
    name: archive
    description: How to package the run into a COMBINE/OMEX archive — the single supplementary
      artifact from which every figure, number and caption regenerates. Unset means
      no archive is emitted.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - StudyCollection
    range: ArchiveConfig
    inlined: true
class_uri: tvbo:StudyCollection

```
</details>

### Induced

<details>
```yaml
name: StudyCollection
description: 'The whole manuscript as one runnable specification: a study that aggregates
  the member studies a paper reports (``members``) and also owns the paper''s own
  demonstration experiments, analyses and figures (the SimulationStudy slots it inherits).
  ``tvbo run`` walks the members and the owned content, emits every reported number
  to a results manifest (``results``) and every figure with its composed caption,
  then packages the lot as a COMBINE/OMEX archive (``archive``) — so the paper becomes
  an instance of the reproducibility it argues for. A Study-of-studies, which no SimulationStudy
  is (``experiments`` ranges over experiments, not studies); legitimized by COMBINE/OMEX,
  SED-ML and the ISA ``Investigation`` top-level container it parallels.'
from_schema: https://w3id.org/tvbo
is_a: SimulationStudy
attributes:
  members:
    name: members
    description: The member studies this collection aggregates, each a reference to
      a study recipe (``recipe``) plus whether it is ``optional`` (skipped unless
      requested, for runs too heavy to recompute per build). ``tvbo run`` executes
      each member's own experiments, analyses and figures; the ``figures``/``analyses``
      inherited here are instead the paper-native demos that belong to no member.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - StudyCollection
    range: StudyMember
    multivalued: true
    inlined: true
    inlined_as_list: true
  results:
    name: results
    description: The named numbers the prose cites, each keyed by the manuscript token
      that stands in for it (``key``) and bound either to a computed value (``used:``
      a DataRef into a member's or its own analysis) or to an authored constant quoted
      from prior work (``value`` + ``source``). ``tvbo run`` collects these into a
      results manifest the document reads, so no reported figure is transcribed by
      hand and a stale or missing key fails the build rather than printing a wrong
      number.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - StudyCollection
    range: ResultBinding
    multivalued: true
    inlined: true
    inlined_as_list: true
  archive:
    name: archive
    description: How to package the run into a COMBINE/OMEX archive — the single supplementary
      artifact from which every figure, number and caption regenerates. Unset means
      no archive is emitted.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - StudyCollection
    range: ArchiveConfig
    inlined: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: StudyCollection
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - Figure
    - Panel
    - Inset
    - Layer
    - 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
    - StudyMember
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  derived_from:
    name: derived_from
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    owner: StudyCollection
    domain_of:
    - Provenance
    - SimulationStudy
    range: string
  model:
    name: model
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - Electrode
    - SimulationExperiment
    - SimulationStudy
    range: Dynamics
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:references
    owner: StudyCollection
    domain_of:
    - Provenance
    - Observation
    - Dynamics
    - SimulationExperiment
    - SimulationStudy
    range: string
    multivalued: true
  key:
    name: key
    description: Deprecated alias of the inherited ``citekey``; retained for back-compatibility
      with existing tooling.
    from_schema: https://w3id.org/tvbo
    owner: StudyCollection
    domain_of:
    - DataSource
    - SimulationStudy
    - ResultBinding
    range: string
  sample:
    name: sample
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - SimulationStudy
    range: Sample
  workflow:
    name: workflow
    description: Study-wide default orchestration for rendering its experiments' sweeps
      into distributed workflows (Slurm/Snakemake/Nextflow). Individual experiments
      refine it via ``workflow_overrides``.
    from_schema: https://w3id.org/tvbo
    owner: StudyCollection
    domain_of:
    - DistributionConfig
    - SimulationExperiment
    - SimulationStudy
    range: WorkflowConfig
    inlined: true
  simulation_experiments:
    name: simulation_experiments
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: experiments
    owner: StudyCollection
    domain_of:
    - SimulationStudy
    range: SimulationExperiment
    multivalued: true
    inlined: true
    inlined_as_list: true
  analyses:
    name: analyses
    description: 'Analyses of this study''s results, each persisted as its own container
      and so bindable by a figure or a later analysis exactly like a run. These take
      the ``Analysis`` form that invokes a ``callable`` over ``arguments`` (the ``type``/``target``/``wrt``
      form analyses a solve and belongs on an ``Observation`` instead), and each needs
      a unique ``name`` — it keys the container. An argument''s ``used:`` DataRef
      both records what was consumed and orders the run: ``tvbo run`` executes the
      analyses around the experiments — one an experiment consumes first, one consuming
      an experiment after — and then renders the figures.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - SimulationStudy
    range: Analysis
    multivalued: true
    inlined: true
    inlined_as_list: true
  figures:
    name: figures
    description: Declarative Figure specs rendered from this study's experiment results
      — closes the replication loop (a study is its experiments plus the figures that
      read them).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - SimulationStudy
    range: Figure
    multivalued: true
    inlined: true
    inlined_as_list: true
  code_source:
    name: code_source
    description: 'Where this study''s callable code lives — the builders and transform/observation
      callables it references by bare ``module:`` name. Decouples the specification
      from its code: a local directory (relative to the recipe YAML or absolute) or
      a git repository fetched and cached at load time. When absent, the conventional
      ``<recipe-dir>/code/`` is used.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - SimulationStudy
    range: CodeSource
    inlined: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: StudyCollection
    domain_of:
    - Dataset
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - 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
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  citekey:
    name: citekey
    description: BibTeX citation key; the join key into references.bib for full bibliographic
      detail. A study is identified by its key/citekey and described by its title
      — no ``name`` needed.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - Study
    range: string
  type:
    name: type
    description: Publication type (article, book, inproceedings, …).
    from_schema: https://w3id.org/tvbo
    owner: StudyCollection
    domain_of:
    - GraphGenerator
    - ProcedureStep
    - File
    - Analysis
    - Aggregation
    - TuningObjective
    - Algorithm
    - Study
    range: string
  title:
    name: title
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:title
    owner: StudyCollection
    domain_of:
    - Study
    range: string
  authors:
    name: authors
    description: Author display strings (full detail in references.bib).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: StudyCollection
    domain_of:
    - Study
    range: string
    multivalued: true
  year:
    name: year
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:issued
    owner: StudyCollection
    domain_of:
    - Study
    range: integer
  doi:
    name: doi
    from_schema: https://w3id.org/tvbo
    slot_uri: bibo:doi
    owner: StudyCollection
    domain_of:
    - SoftwarePackage
    - Study
    range: string
class_uri: tvbo:StudyCollection

```
</details></div>