Class: CoordinateSet

A group of coordinates reported together -- a row group of a table, or a run of sentences in the text -- and what it is for. The coordinates stay in the parse, as for tables; this records their role and links them to what they belong to: the analysis a result reports, the regions an anchor locates.

A set has one role: its dominant one. The groups come from the table parse, which splits a table by what was tested rather than by what each row is for, so a set can mix roles -- a connectivity results table that lists its own seed as a row. Such a set keeps the role of most of its points, and the odd point takes that role with it. This is a known error, about 1.3% of sets, accepted rather than splitting the parse's groups.

URI: neurostudy_ex:CoordinateSet

 classDiagram
    class CoordinateSet
    click CoordinateSet href "../CoordinateSet/"
      CoordinateSet : analysis





        CoordinateSet --> "0..1" Analysis : analysis
        click Analysis href "../Analysis/"



      CoordinateSet : anchor_kind





        CoordinateSet --> "0..1" ExtractedAnchorKind : anchor_kind
        click ExtractedAnchorKind href "../ExtractedAnchorKind/"



      CoordinateSet : description





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



      CoordinateSet : local_id

      CoordinateSet : regions





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



      CoordinateSet : result_kind





        CoordinateSet --> "0..1" ExtractedResultKind : result_kind
        click ExtractedResultKind href "../ExtractedResultKind/"



      CoordinateSet : role





        CoordinateSet --> "0..1" ExtractedCoordinateRole : role
        click ExtractedCoordinateRole href "../ExtractedCoordinateRole/"



      CoordinateSet : stable_id

Slots

Name	Cardinality and Range	Description	Inheritance
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	The key the coordinate parse gave this set, `ParsedAnalysis	direct
role	0..1 ExtractedCoordinateRole	What these coordinates are for	direct
result_kind	0..1 ExtractedResultKind	For a result, the kind of analysis that produced it	direct
anchor_kind	0..1 ExtractedAnchorKind	For an anchor, what it defines	direct
analysis	0..1 Analysis	For a result, the analysis whose findings these are	direct
regions	* Region	For an anchor, the regions these coordinates locate	direct
description	0..1 ExtractedString	What the set is, in the source's words, when the role alone does not say	direct

Usages

used by	used in	type	used
Study	coordinate_sets	range	CoordinateSet

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: CoordinateSet
description: 'A group of coordinates reported together -- a row group of a table,
  or a run of sentences in the text -- and what it is for. The coordinates stay in
  the parse, as for tables; this records their role and links them to what they belong
  to: the analysis a result reports, the regions an anchor locates.

  A set has one role: its dominant one. The groups come from the table parse, which
  splits a table by what was tested rather than by what each row is for, so a set
  can mix roles -- a connectivity results table that lists its own seed as a row.
  Such a set keeps the role of most of its points, and the odd point takes that role
  with it. This is a known error, about 1.3% of sets, accepted rather than splitting
  the parse''s groups.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  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/analysis
    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: 'The key the coordinate parse gave this set, `ParsedAnalysis.key`
      in neuroimaging-paper-parse: `analysis#<h>`, the same key `Analysis.source_table_analysis`
      names, where `h` hashes the set''s name, space and points, so the key survives
      a re-parse that extracts the same set.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    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
  role:
    name: role
    description: What these coordinates are for.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: ExtractedCoordinateRole
  result_kind:
    name: result_kind
    description: For a `result`, the kind of analysis that produced it. Absent for
      every other role.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: ExtractedResultKind
  anchor_kind:
    name: anchor_kind
    description: For an `anchor`, what it defines. Absent for every other role.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: ExtractedAnchorKind
  analysis:
    name: analysis
    description: For a `result`, the analysis whose findings these are. The same join
      `Analysis.source_table_analysis` makes from the other side, here for sets read
      from the text as well.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: Analysis
    inlined: false
  regions:
    name: regions
    description: For an `anchor`, the regions these coordinates locate.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    domain_of:
    - Analysis
    - FactorLevel
    - CoordinateSet
    - Study
    range: Region
    multivalued: true
    inlined: false
  description:
    name: description
    description: What the set is, in the source's words, when the role alone does
      not say.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString

Induced

name: CoordinateSet
description: 'A group of coordinates reported together -- a row group of a table,
  or a run of sentences in the text -- and what it is for. The coordinates stay in
  the parse, as for tables; this records their role and links them to what they belong
  to: the analysis a result reports, the regions an anchor locates.

  A set has one role: its dominant one. The groups come from the table parse, which
  splits a table by what was tested rather than by what each row is for, so a set
  can mix roles -- a connectivity results table that lists its own seed as a row.
  Such a set keeps the role of most of its points, and the odd point takes that role
  with it. This is a known error, about 1.3% of sets, accepted rather than splitting
  the parse''s groups.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  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/analysis
    owner: CoordinateSet
    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: 'The key the coordinate parse gave this set, `ParsedAnalysis.key`
      in neuroimaging-paper-parse: `analysis#<h>`, the same key `Analysis.source_table_analysis`
      names, where `h` hashes the set''s name, space and points, so the key survives
      a re-parse that extracts the same set.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    identifier: true
    owner: CoordinateSet
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  role:
    name: role
    description: What these coordinates are for.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: ExtractedCoordinateRole
  result_kind:
    name: result_kind
    description: For a `result`, the kind of analysis that produced it. Absent for
      every other role.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: ExtractedResultKind
  anchor_kind:
    name: anchor_kind
    description: For an `anchor`, what it defines. Absent for every other role.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: ExtractedAnchorKind
  analysis:
    name: analysis
    description: For a `result`, the analysis whose findings these are. The same join
      `Analysis.source_table_analysis` makes from the other side, here for sets read
      from the text as well.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: Analysis
    inlined: false
  regions:
    name: regions
    description: For an `anchor`, the regions these coordinates locate.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    owner: CoordinateSet
    domain_of:
    - Analysis
    - FactorLevel
    - CoordinateSet
    - Study
    range: Region
    multivalued: true
    inlined: false
  description:
    name: description
    description: What the set is, in the source's words, when the role alone does
      not say.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    owner: CoordinateSet
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString