Reference·Classes

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.

URI: tvbo:StudyCollection

 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
  • SimulationStudy
    • StudyCollection

Class Properties

Property	Value
Class URI	tvbo:StudyCollection

Slots

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

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

Direct

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

Induced

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