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:CoordinateSet

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





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



      CoordinateSet : anchor_kind

      CoordinateSet : description

      CoordinateSet : id

      CoordinateSet : regions





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



      CoordinateSet : result_kind

      CoordinateSet : role

      CoordinateSet : table





        CoordinateSet --> "0..1" Table : table
        click Table href "../Table/"



      CoordinateSet : text_excerpt

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 String	The key the coordinate parse gave this set, `ParsedAnalysis	direct
table	0..1 Table	The table this set was read from	direct
text_excerpt	0..1 String	For a set read from the text, the sentences it was read from: the sentence ho...	direct
role	0..1 String or  CoordinateRole	What these coordinates are for	direct
result_kind	0..1 String or  ResultKind	For a result, the kind of analysis that produced it	direct
anchor_kind	0..1 String or  AnchorKind	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 String	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-storage

Mappings

Mapping Type	Mapped Value
self	neurostudy:CoordinateSet
native	neurostudy: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-storage
rank: 1000
attributes:
  id:
    name: 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.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    identifier: true
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  table:
    name: table
    description: The table this set was read from. Absent for a set read from the
      text.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: Table
    inlined: false
  text_excerpt:
    name: text_excerpt
    description: 'For a set read from the text, the sentences it was read from: the
      sentence holding the coordinates and its neighbours, extended past any neighbour
      that also holds coordinates.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: string
  role:
    name: role
    description: What these coordinates are for.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    any_of:
    - range: CoordinateRole
    - range: string
  result_kind:
    name: result_kind
    description: For a `result`, the kind of analysis that produced it. Absent for
      every other role.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    any_of:
    - range: ResultKind
    - range: string
  anchor_kind:
    name: anchor_kind
    description: For an `anchor`, what it defines. Absent for every other role.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    any_of:
    - range: AnchorKind
    - range: string
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    domain_of:
    - CoordinateSet
    range: Analysis
    inlined: false
  regions:
    name: regions
    description: For an `anchor`, the regions these coordinates locate.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string

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-storage
rank: 1000
attributes:
  id:
    name: 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.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    identifier: true
    owner: CoordinateSet
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  table:
    name: table
    description: The table this set was read from. Absent for a set read from the
      text.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: Table
    inlined: false
  text_excerpt:
    name: text_excerpt
    description: 'For a set read from the text, the sentences it was read from: the
      sentence holding the coordinates and its neighbours, extended past any neighbour
      that also holds coordinates.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: string
  role:
    name: role
    description: What these coordinates are for.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: string
    any_of:
    - range: CoordinateRole
    - range: string
  result_kind:
    name: result_kind
    description: For a `result`, the kind of analysis that produced it. Absent for
      every other role.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: string
    any_of:
    - range: ResultKind
    - range: string
  anchor_kind:
    name: anchor_kind
    description: For an `anchor`, what it defines. Absent for every other role.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: string
    any_of:
    - range: AnchorKind
    - range: string
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    rank: 1000
    owner: CoordinateSet
    domain_of:
    - CoordinateSet
    range: Analysis
    inlined: false
  regions:
    name: regions
    description: For an `anchor`, the regions these coordinates locate.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/analysis
    owner: CoordinateSet
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string