Class: Study

The publication-level record that contains the groups, tasks, design, acquisitions, preprocessing pipelines, model estimations, analyses, and reported result tables belonging to one study. Conditions belong to the task they are part of, not to the study.

URI: neurostudy_ex:Study

 classDiagram
    class Study
    click Study href "../Study/"
      Study : acquisitions





        Study --> "*" Acquisition : acquisitions
        click Acquisition href "../Acquisition/"



      Study : analyses





        Study --> "*" Analysis : analyses
        click Analysis href "../Analysis/"



      Study : assessments





        Study --> "*" Assessment : assessments
        click Assessment href "../Assessment/"



      Study : coordinate_sets





        Study --> "*" CoordinateSet : coordinate_sets
        click CoordinateSet href "../CoordinateSet/"



      Study : description





        Study --> "0..1" ExtractedString : description
        click ExtractedString href "../ExtractedString/"



      Study : design





        Study --> "0..1" StudyDesign : design
        click StudyDesign href "../StudyDesign/"



      Study : devices





        Study --> "*" Device : devices
        click Device href "../Device/"



      Study : external_datasets





        Study --> "*" ExternalDataset : external_datasets
        click ExternalDataset href "../ExternalDataset/"



      Study : extraction_metadata





        Study --> "1" ExtractionMetadata : extraction_metadata
        click ExtractionMetadata href "../ExtractionMetadata/"



      Study : groups





        Study --> "*" Group : groups
        click Group href "../Group/"



      Study : hypothesis





        Study --> "0..1" ExtractedStringList : hypothesis
        click ExtractedStringList href "../ExtractedStringList/"



      Study : inference_settings





        Study --> "*" InferenceSettings : inference_settings
        click InferenceSettings href "../InferenceSettings/"



      Study : local_id

      Study : measures





        Study --> "*" Measure : measures
        click Measure href "../Measure/"



      Study : model_estimations





        Study --> "*" ModelEstimation : model_estimations
        click ModelEstimation href "../ModelEstimation/"



      Study : preprocessings





        Study --> "*" Preprocessing : preprocessings
        click Preprocessing href "../Preprocessing/"



      Study : regions





        Study --> "*" Region : regions
        click Region href "../Region/"



      Study : result_reporting





        Study --> "0..1" ExtractedResultReporting : result_reporting
        click ExtractedResultReporting href "../ExtractedResultReporting/"



      Study : stable_id

      Study : tables





        Study --> "*" Table : tables
        click Table href "../Table/"



      Study : tasks





        Study --> "*" Task : tasks
        click Task href "../Task/"

Class Properties

Property	Value
Tree Root	Yes

Slots

Name	Cardinality and Range	Description	Inheritance
extraction_metadata	1 ExtractionMetadata	Provenance for this extraction record	direct
stable_id	0..1 String	UUID minted by the store the first time this entity appears, never by an extr...	direct
local_id	1 String	Stable identifier for the study record, such as a DOI-based or repository-loc...	direct
description	0..1 ExtractedString	Brief free-text summary of the study aims and scope	direct
hypothesis	0..1 ExtractedStringList	The study's own statement of what it expected to find, quoted from the paper ...	direct
design	0..1 StudyDesign	The study's design outside its tasks: how participants were assigned, the arm...	direct
groups	* Group	Participant or demographic groups	direct
tasks	* Task	Task, resting-state, stimulation, passive-viewing, or other meaningful partic...	direct
assessments	* Assessment	Measures of participants that were taken independently of an acquisition	direct
regions	* Region	Brain regions the study delimited and then used -- as connectivity seeds or t...	direct
devices	* Device	The scanners, amplifiers, or recording systems the study collected data on	direct
acquisitions	* Acquisition	Image or signal acquisition protocols used in the study	direct
preprocessings	* Preprocessing	Preprocessing pipelines applied before statistical analysis	direct
model_estimations	* ModelEstimation	Model estimation records used by one or more analyses	direct
inference_settings	* InferenceSettings	Thresholding and correction schemes used by one or more analyses	direct
measures	* Measure	The scientific quantities the study measured, used by one or more analyses	direct
analyses	* Analysis	Distinct analyses or inferential tests reported by the study, including those...	direct
result_reporting	0..1 ExtractedResultReporting	Whether the paper reports inferential analyses of its own	direct
tables	* Table	Publication tables from which results or analysis metadata were extracted	direct
coordinate_sets	* CoordinateSet	Every group of coordinates the paper reports, in its tables or its text, with...	direct
external_datasets	* ExternalDataset	Named external datasets used, cited, or made available by the study	direct

Identifier and Mapping Information

Schema Source

• from schema: https://neurostuff.org/schemas/neuroimaging-study-extraction

Mappings

Mapping Type	Mapped Value
self	neurostudy_ex:Study
native	neurostudy_ex:Study

LinkML Source

Direct

name: Study
description: The publication-level record that contains the groups, tasks, design,
  acquisitions, preprocessing pipelines, model estimations, analyses, and reported
  result tables belonging to one study. Conditions belong to the task they are part
  of, not to the study.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  extraction_metadata:
    name: extraction_metadata
    description: Provenance for this extraction record.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: ExtractionMetadata
    required: true
    inlined: true
  stable_id:
    name: stable_id
    description: UUID minted by the store the first time this entity appears, never
      by an extractor, and kept across re-runs so a later extraction matches the same
      entity.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  local_id:
    name: local_id
    description: Stable identifier for the study record, such as a DOI-based or repository-local
      identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    identifier: true
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  description:
    name: description
    description: Brief free-text summary of the study aims and scope.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString
  hypothesis:
    name: hypothesis
    description: 'The study''s own statement of what it expected to find, quoted from
      the paper -- usually the closing paragraph of the Introduction, in the form
      "we hypothesized that" or "we predicted that". Verbatim but for citation markers,
      one entry per prediction, so a study stating several gets several.

      A prediction, not a purpose. "The aim of this study was to examine whether connectivity
      differs between patients and controls" says what was tested and takes no value
      here; "we expected connectivity to be lower in patients" says what was expected
      and does. Recording an aim as a hypothesis asserts a direction the study never
      committed to, which is precisely what a reader consults this field to check.

      Absent when the paper states no prediction, which is common: never paraphrase
      an aim, an abstract sentence, or a finding into one. Where the only statement
      is in the Discussion -- "consistent with our hypothesis that connectivity would
      be lower" -- quote that clause, which is still the study''s account of what
      it predicted rather than `Analysis.interpretations`, the source''s account of
      what it found.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: ExtractedStringList
  design:
    name: design
    description: 'The study''s design outside its tasks: how participants were assigned,
      the arms they were assigned to, and the occasions data were collected on. The
      narrative design description is this record''s own `description`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: StudyDesign
    inlined: true
  groups:
    name: groups
    description: Participant or demographic groups.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - FactorLevel
    - Study
    range: Group
    multivalued: true
    inlined_as_list: true
  tasks:
    name: tasks
    description: Task, resting-state, stimulation, passive-viewing, or other meaningful
      participant paradigms associated with study acquisitions. Each holds the conditions
      it was made of.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - Study
    range: Task
    multivalued: true
    inlined_as_list: true
  assessments:
    name: assessments
    description: Measures of participants that were taken independently of an acquisition.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - Study
    range: Assessment
    multivalued: true
    inlined_as_list: true
  regions:
    name: regions
    description: Brain regions the study delimited and then used -- as connectivity
      seeds or targets, as the search space an analysis was restricted to, as the
      levels of a factor comparing regions, or as the signal a model term carries.
      Declared here once and referenced by identifier wherever used.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - FactorLevel
    - CoordinateSet
    - Study
    range: Region
    multivalued: true
    inlined_as_list: true
  devices:
    name: devices
    description: The scanners, amplifiers, or recording systems the study collected
      data on. Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: Device
    multivalued: true
    inlined_as_list: true
  acquisitions:
    name: acquisitions
    description: Image or signal acquisition protocols used in the study.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Task
    - Analysis
    - Study
    range: Acquisition
    multivalued: true
    inlined_as_list: true
  preprocessings:
    name: preprocessings
    description: Preprocessing pipelines applied before statistical analysis.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: Preprocessing
    multivalued: true
    inlined_as_list: true
  model_estimations:
    name: model_estimations
    description: Model estimation records used by one or more analyses.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: ModelEstimation
    multivalued: true
    inlined_as_list: true
  inference_settings:
    name: inference_settings
    description: Thresholding and correction schemes used by one or more analyses.
      Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - Study
    range: InferenceSettings
    multivalued: true
    inlined_as_list: true
  measures:
    name: measures
    description: The scientific quantities the study measured, used by one or more
      analyses. Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: Measure
    multivalued: true
    inlined_as_list: true
  analyses:
    name: analyses
    description: 'Distinct analyses or inferential tests reported by the study, including
      those that found nothing (`Analysis.outcome: no_significant_effect`) and those
      reported without coordinates. Whether an empty list means the paper reports
      none is `result_reporting`''s to say, not the list''s.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: Analysis
    multivalued: true
    inlined_as_list: true
  result_reporting:
    name: result_reporting
    description: 'Whether the paper reports inferential analyses of its own. An empty
      `analyses` list is otherwise ambiguous: a methods or data paper that tests nothing
      and a paper the extractor read badly look the same. With this set, `no_analyses_reported`
      asserts the emptiness, with the sentences that show it as evidence.

      Says nothing about whether the analyses found anything; that is each `Analysis.outcome`,
      summarised in `outcome_summary`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: ExtractedResultReporting
  tables:
    name: tables
    description: Publication tables from which results or analysis metadata were extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    domain_of:
    - Analysis
    - Study
    range: Table
    multivalued: true
    inlined_as_list: true
  coordinate_sets:
    name: coordinate_sets
    description: Every group of coordinates the paper reports, in its tables or its
      text, with what each is for.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: CoordinateSet
    multivalued: true
    inlined_as_list: true
  external_datasets:
    name: external_datasets
    description: Named external datasets used, cited, or made available by the study.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    domain_of:
    - Study
    range: ExternalDataset
    multivalued: true
    inlined_as_list: true
tree_root: true

Induced

name: Study
description: The publication-level record that contains the groups, tasks, design,
  acquisitions, preprocessing pipelines, model estimations, analyses, and reported
  result tables belonging to one study. Conditions belong to the task they are part
  of, not to the study.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  extraction_metadata:
    name: extraction_metadata
    description: Provenance for this extraction record.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: ExtractionMetadata
    required: true
    inlined: true
  stable_id:
    name: stable_id
    description: UUID minted by the store the first time this entity appears, never
      by an extractor, and kept across re-runs so a later extraction matches the same
      entity.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  local_id:
    name: local_id
    description: Stable identifier for the study record, such as a DOI-based or repository-local
      identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    identifier: true
    owner: Study
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  description:
    name: description
    description: Brief free-text summary of the study aims and scope.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString
  hypothesis:
    name: hypothesis
    description: 'The study''s own statement of what it expected to find, quoted from
      the paper -- usually the closing paragraph of the Introduction, in the form
      "we hypothesized that" or "we predicted that". Verbatim but for citation markers,
      one entry per prediction, so a study stating several gets several.

      A prediction, not a purpose. "The aim of this study was to examine whether connectivity
      differs between patients and controls" says what was tested and takes no value
      here; "we expected connectivity to be lower in patients" says what was expected
      and does. Recording an aim as a hypothesis asserts a direction the study never
      committed to, which is precisely what a reader consults this field to check.

      Absent when the paper states no prediction, which is common: never paraphrase
      an aim, an abstract sentence, or a finding into one. Where the only statement
      is in the Discussion -- "consistent with our hypothesis that connectivity would
      be lower" -- quote that clause, which is still the study''s account of what
      it predicted rather than `Analysis.interpretations`, the source''s account of
      what it found.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: ExtractedStringList
  design:
    name: design
    description: 'The study''s design outside its tasks: how participants were assigned,
      the arms they were assigned to, and the occasions data were collected on. The
      narrative design description is this record''s own `description`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: StudyDesign
    inlined: true
  groups:
    name: groups
    description: Participant or demographic groups.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - FactorLevel
    - Study
    range: Group
    multivalued: true
    inlined: true
    inlined_as_list: true
  tasks:
    name: tasks
    description: Task, resting-state, stimulation, passive-viewing, or other meaningful
      participant paradigms associated with study acquisitions. Each holds the conditions
      it was made of.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - Study
    range: Task
    multivalued: true
    inlined: true
    inlined_as_list: true
  assessments:
    name: assessments
    description: Measures of participants that were taken independently of an acquisition.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - Study
    range: Assessment
    multivalued: true
    inlined: true
    inlined_as_list: true
  regions:
    name: regions
    description: Brain regions the study delimited and then used -- as connectivity
      seeds or targets, as the search space an analysis was restricted to, as the
      levels of a factor comparing regions, or as the signal a model term carries.
      Declared here once and referenced by identifier wherever used.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - FactorLevel
    - CoordinateSet
    - Study
    range: Region
    multivalued: true
    inlined: true
    inlined_as_list: true
  devices:
    name: devices
    description: The scanners, amplifiers, or recording systems the study collected
      data on. Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: Device
    multivalued: true
    inlined: true
    inlined_as_list: true
  acquisitions:
    name: acquisitions
    description: Image or signal acquisition protocols used in the study.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Task
    - Analysis
    - Study
    range: Acquisition
    multivalued: true
    inlined: true
    inlined_as_list: true
  preprocessings:
    name: preprocessings
    description: Preprocessing pipelines applied before statistical analysis.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: Preprocessing
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_estimations:
    name: model_estimations
    description: Model estimation records used by one or more analyses.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: ModelEstimation
    multivalued: true
    inlined: true
    inlined_as_list: true
  inference_settings:
    name: inference_settings
    description: Thresholding and correction schemes used by one or more analyses.
      Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - Study
    range: InferenceSettings
    multivalued: true
    inlined: true
    inlined_as_list: true
  measures:
    name: measures
    description: The scientific quantities the study measured, used by one or more
      analyses. Declared here once and referenced by identifier.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: Measure
    multivalued: true
    inlined: true
    inlined_as_list: true
  analyses:
    name: analyses
    description: 'Distinct analyses or inferential tests reported by the study, including
      those that found nothing (`Analysis.outcome: no_significant_effect`) and those
      reported without coordinates. Whether an empty list means the paper reports
      none is `result_reporting`''s to say, not the list''s.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: Analysis
    multivalued: true
    inlined: true
    inlined_as_list: true
  result_reporting:
    name: result_reporting
    description: 'Whether the paper reports inferential analyses of its own. An empty
      `analyses` list is otherwise ambiguous: a methods or data paper that tests nothing
      and a paper the extractor read badly look the same. With this set, `no_analyses_reported`
      asserts the emptiness, with the sentences that show it as evidence.

      Says nothing about whether the analyses found anything; that is each `Analysis.outcome`,
      summarised in `outcome_summary`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: ExtractedResultReporting
  tables:
    name: tables
    description: Publication tables from which results or analysis metadata were extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    owner: Study
    domain_of:
    - Analysis
    - Study
    range: Table
    multivalued: true
    inlined: true
    inlined_as_list: true
  coordinate_sets:
    name: coordinate_sets
    description: Every group of coordinates the paper reports, in its tables or its
      text, with what each is for.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: CoordinateSet
    multivalued: true
    inlined: true
    inlined_as_list: true
  external_datasets:
    name: external_datasets
    description: Named external datasets used, cited, or made available by the study.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/study
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: ExternalDataset
    multivalued: true
    inlined: true
    inlined_as_list: true
tree_root: true