Class: CoordinateParse

Every coordinate a paper reports, grouped into analyses. An original parse is written by the ingestion workflow; a revision is written by pondie when its audit disagrees with the original.

A parse is never edited after it is written. A reader that disagrees with it writes a revision instead, and the revision is a complete parse on its own: neurostore can store it as a new version of the paper's analyses without consulting the parse it revises.

Analyses that pondie accepts or relabels keep their keys, because their name, space and points are unchanged, so claims made against them carry over to the revision untouched. Only a split, a merge or an omission changes which keys exist.

URI: parse:CoordinateParse

 classDiagram
    class CoordinateParse
    click CoordinateParse href "../CoordinateParse/"
      CoordinateParse : analyses





        CoordinateParse --> "1..*" ParsedAnalysis : analyses
        click ParsedAnalysis href "../ParsedAnalysis/"



      CoordinateParse : header





        CoordinateParse --> "1" ArtifactHeader : header
        click ArtifactHeader href "../ArtifactHeader/"



      CoordinateParse : omitted_analyses





        CoordinateParse --> "*" OmittedAnalysis : omitted_analyses
        click OmittedAnalysis href "../OmittedAnalysis/"



      CoordinateParse : parse_id

      CoordinateParse : revision_of

      CoordinateParse : tables





        CoordinateParse --> "*" TableReading : tables
        click TableReading href "../TableReading/"



      CoordinateParse : text_sha256

      CoordinateParse : text_sweep





        CoordinateParse --> "0..1" TextSweep : text_sweep
        click TextSweep href "../TextSweep/"



      CoordinateParse : verdicts





        CoordinateParse --> "*" AnalysisVerdict : verdicts
        click AnalysisVerdict href "../AnalysisVerdict/"

Slots

Name	Cardinality and Range	Description	Inheritance
header	1 ArtifactHeader	inputs names the parsed paper by text_sha256, and for a revision also the...	direct
parse_id	1 String	This parse's identity, the fingerprint every later artifact cites	direct
text_sha256	1 String	The parsed paper's fingerprint	direct
revision_of	0..1 String	The parse_id of the parse this one revises	direct
analyses	1..* ParsedAnalysis	May be empty: the parse ran and found no analysis	direct
tables	* TableReading	One entry per table of the parsed paper: what reading it for coordinates foun...	direct
omitted_analyses	* OmittedAnalysis	Text or figure analyses the producer read and left out of analyses, each wi...	direct
text_sweep	0..1 TextSweep	How much of the text was searched for coordinates outside tables	direct
verdicts	* AnalysisVerdict	On a revision only: one verdict for every analysis of the revised parse, so n...	direct

Identifier and Mapping Information

Schema Source

• from schema: https://neurostuff.org/schemas/neuroimaging-paper-parse

Mappings

Mapping Type	Mapped Value
self	parse:CoordinateParse
native	parse:CoordinateParse

LinkML Source

Direct

name: CoordinateParse
description: 'Every coordinate a paper reports, grouped into analyses. An original
  parse is written by the ingestion workflow; a revision is written by pondie when
  its audit disagrees with the original.

  A parse is never edited after it is written. A reader that disagrees with it writes
  a revision instead, and the revision is a complete parse on its own: neurostore
  can store it as a new version of the paper''s analyses without consulting the parse
  it revises.

  Analyses that pondie accepts or relabels keep their keys, because their name, space
  and points are unchanged, so claims made against them carry over to the revision
  untouched. Only a split, a merge or an omission changes which keys exist.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  header:
    name: header
    description: '`inputs` names the parsed paper by `text_sha256`, and for a revision
      also the parse it revises by `parse_id`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ArtifactHeader
    required: true
    inlined: true
  parse_id:
    name: parse_id
    description: This parse's identity, the fingerprint every later artifact cites.
      Unique per paper; a sha256 of the canonical JSON of `analyses` is recommended,
      so two producers that reach the same analyses reach the same id.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: string
    required: true
  text_sha256:
    name: text_sha256
    description: The parsed paper's fingerprint. Every point's cells and spans address
      it.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: string
    required: true
  revision_of:
    name: revision_of
    description: The `parse_id` of the parse this one revises. Absent on an original
      parse, which is how a reader tells the two apart.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: string
  analyses:
    name: analyses
    description: 'May be empty: the parse ran and found no analysis. A paper the parse
      never ran on has no CoordinateParse at all, so the two are never confused, and
      `tables` says what reading each table found.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: ParsedAnalysis
    required: true
    multivalued: true
    inlined_as_list: true
  tables:
    name: tables
    description: 'One entry per table of the parsed paper: what reading it for coordinates
      found, or why it was not read. A table with no entry was not considered.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: TableReading
    multivalued: true
    inlined_as_list: true
  omitted_analyses:
    name: omitted_analyses
    description: Text or figure analyses the producer read and left out of `analyses`,
      each with the reason. A table's omissions are in `tables`. Absent when nothing
      was left out.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: OmittedAnalysis
    multivalued: true
    inlined_as_list: true
  text_sweep:
    name: text_sweep
    description: How much of the text was searched for coordinates outside tables.
      Absent when the text was not searched.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: TextSweep
    inlined: true
  verdicts:
    name: verdicts
    description: 'On a revision only: one verdict for every analysis of the revised
      parse, so nothing in it is silently dropped, and an `add` verdict for every
      analysis the revision introduces that the revised parse lacked. An original
      parse has none.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    domain_of:
    - CoordinateParse
    range: AnalysisVerdict
    multivalued: true
    inlined_as_list: true

Induced

name: CoordinateParse
description: 'Every coordinate a paper reports, grouped into analyses. An original
  parse is written by the ingestion workflow; a revision is written by pondie when
  its audit disagrees with the original.

  A parse is never edited after it is written. A reader that disagrees with it writes
  a revision instead, and the revision is a complete parse on its own: neurostore
  can store it as a new version of the paper''s analyses without consulting the parse
  it revises.

  Analyses that pondie accepts or relabels keep their keys, because their name, space
  and points are unchanged, so claims made against them carry over to the revision
  untouched. Only a split, a merge or an omission changes which keys exist.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  header:
    name: header
    description: '`inputs` names the parsed paper by `text_sha256`, and for a revision
      also the parse it revises by `parse_id`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    owner: CoordinateParse
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ArtifactHeader
    required: true
    inlined: true
  parse_id:
    name: parse_id
    description: This parse's identity, the fingerprint every later artifact cites.
      Unique per paper; a sha256 of the canonical JSON of `analyses` is recommended,
      so two producers that reach the same analyses reach the same id.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: string
    required: true
  text_sha256:
    name: text_sha256
    description: The parsed paper's fingerprint. Every point's cells and spans address
      it.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    owner: CoordinateParse
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: string
    required: true
  revision_of:
    name: revision_of
    description: The `parse_id` of the parse this one revises. Absent on an original
      parse, which is how a reader tells the two apart.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: string
  analyses:
    name: analyses
    description: 'May be empty: the parse ran and found no analysis. A paper the parse
      never ran on has no CoordinateParse at all, so the two are never confused, and
      `tables` says what reading each table found.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: ParsedAnalysis
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  tables:
    name: tables
    description: 'One entry per table of the parsed paper: what reading it for coordinates
      found, or why it was not read. A table with no entry was not considered.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    owner: CoordinateParse
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: TableReading
    multivalued: true
    inlined: true
    inlined_as_list: true
  omitted_analyses:
    name: omitted_analyses
    description: Text or figure analyses the producer read and left out of `analyses`,
      each with the reason. A table's omissions are in `tables`. Absent when nothing
      was left out.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: OmittedAnalysis
    multivalued: true
    inlined: true
    inlined_as_list: true
  text_sweep:
    name: text_sweep
    description: How much of the text was searched for coordinates outside tables.
      Absent when the text was not searched.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: TextSweep
    inlined: true
  verdicts:
    name: verdicts
    description: 'On a revision only: one verdict for every analysis of the revised
      parse, so nothing in it is silently dropped, and an `add` verdict for every
      analysis the revision introduces that the revised parse lacked. An original
      parse has none.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
    rank: 1000
    owner: CoordinateParse
    domain_of:
    - CoordinateParse
    range: AnalysisVerdict
    multivalued: true
    inlined: true
    inlined_as_list: true