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Class: ParsedPaper

One paper as text, tables and bibliographic facts. The same shape for every download source.

The text is the only offset space. Every evidence span an extraction record cites, every table row's position and every text-read point addresses text_sha256's characters, so a span can be checked by slicing the text, and a span made against a different text is detectably wrong.

URI: parse:ParsedPaper

 classDiagram
    class ParsedPaper
    click ParsedPaper href "../ParsedPaper/"
      ParsedPaper : bibliography





        ParsedPaper --> "1" Bibliography : bibliography
        click Bibliography href "../Bibliography/"



      ParsedPaper : citations





        ParsedPaper --> "*" Citation : citations
        click Citation href "../Citation/"



      ParsedPaper : header





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



      ParsedPaper : is_meta_analysis

      ParsedPaper : is_meta_analysis_basis





        ParsedPaper --> "0..1" MetaAnalysisBasis : is_meta_analysis_basis
        click MetaAnalysisBasis href "../MetaAnalysisBasis/"



      ParsedPaper : references





        ParsedPaper --> "*" Reference : references
        click Reference href "../Reference/"



      ParsedPaper : reported_copies





        ParsedPaper --> "*" ReportedCopy : reported_copies
        click ReportedCopy href "../ReportedCopy/"



      ParsedPaper : sections





        ParsedPaper --> "*" Section : sections
        click Section href "../Section/"



      ParsedPaper : source

      ParsedPaper : source_reason

      ParsedPaper : supplements





        ParsedPaper --> "*" Supplement : supplements
        click Supplement href "../Supplement/"



      ParsedPaper : tables





        ParsedPaper --> "*" ParsedTable : tables
        click ParsedTable href "../ParsedTable/"



      ParsedPaper : text_copy





        ParsedPaper --> "1" HeldCopy : text_copy
        click HeldCopy href "../HeldCopy/"



      ParsedPaper : text_length

      ParsedPaper : text_path

      ParsedPaper : text_sha256

Slots

Name Cardinality and Range Description Inheritance
header 1
ArtifactHeader		 direct
source 1
String or 
DocumentSource		 direct
source_reason 0..1
String		 Why this source's text was chosen over the others downloaded, such as "most t... direct
text_copy 1
HeldCopy		 The copy the text was read from direct
reported_copies *
ReportedCopy		 Copies of the paper that a source lists and that we do not hold, each with it... direct
text_path 1
String		 The text file's path, relative to the paper's bundle directory direct
text_sha256 1
String		 sha256 of the text file's UTF-8 bytes direct
text_length 0..1
Integer		 direct
bibliography 1
Bibliography		 direct
is_meta_analysis 1
Boolean		 Whether the paper is itself a meta-analysis or review, decided here once direct
is_meta_analysis_basis 0..1
MetaAnalysisBasis		 direct
sections *
Section		 direct
supplements *
Supplement		 Supplementary material the paper links to, and whether it was fetched direct
references *
Reference		 The paper's reference list, in order direct
citations *
Citation		 Every in-text citation, where it sits in the text and which reference it poin... direct
tables *
ParsedTable		 direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ParsedPaper
description: 'One paper as text, tables and bibliographic facts. The same shape for
  every download source.

  The text is the only offset space. Every evidence span an extraction record cites,
  every table row''s position and every text-read point addresses `text_sha256`''s
  characters, so a span can be checked by slicing the text, and a span made against
  a different text is detectably wrong.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  header:
    name: header
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ArtifactHeader
    required: true
    inlined: true
  source:
    name: source
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    required: true
    any_of:
    - range: DocumentSource
    - range: string
  source_reason:
    name: source_reason
    description: Why this source's text was chosen over the others downloaded, such
      as "most tables" or "first in download order". Every stage reads this one text,
      so the choice is made once and recorded.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: string
  text_copy:
    name: text_copy
    description: The copy the text was read from. Its licence and access, not the
      paper's licence, decide whether the text may be passed on.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: HeldCopy
    required: true
    inlined: true
  reported_copies:
    name: reported_copies
    description: Copies of the paper that a source lists and that we do not hold,
      each with its own licence. Where an open copy is, when `bibliography.oa_status`
      says one exists.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: ReportedCopy
    multivalued: true
    inlined_as_list: true
  text_path:
    name: text_path
    description: The text file's path, relative to the paper's bundle directory.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: string
    required: true
  text_sha256:
    name: text_sha256
    description: sha256 of the text file's UTF-8 bytes. This artifact's fingerprint.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: string
    required: true
  text_length:
    name: text_length
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: integer
    minimum_value: 0
  bibliography:
    name: bibliography
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: Bibliography
    required: true
    inlined: true
  is_meta_analysis:
    name: is_meta_analysis
    description: Whether the paper is itself a meta-analysis or review, decided here
      once. Every consumer reads this field; none applies its own test.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: boolean
    required: true
  is_meta_analysis_basis:
    name: is_meta_analysis_basis
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: MetaAnalysisBasis
  sections:
    name: sections
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: Section
    multivalued: true
    inlined_as_list: true
  supplements:
    name: supplements
    description: Supplementary material the paper links to, and whether it was fetched.
      A result the text cites to a supplement that was not fetched is reported elsewhere,
      not missing.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: Supplement
    multivalued: true
    inlined_as_list: true
  references:
    name: references
    description: The paper's reference list, in order. Usually fetched from an API
      by the paper's identifiers rather than parsed from the text (`Reference.provider`
      says which), so it is complete and carries DOIs even when the text's list is
      badly extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    - Citation
    range: Reference
    multivalued: true
    inlined_as_list: true
  citations:
    name: citations
    description: 'Every in-text citation, where it sits in the text and which reference
      it points to. The link from a sentence to a work, which the reference list alone
      cannot give: what resolves the citations a task''s description makes (storage
      `Task.reference_ids`) and traces a task to the paper that introduced it.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    range: Citation
    multivalued: true
    inlined_as_list: true
  tables:
    name: tables
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ParsedTable
    multivalued: true
    inlined_as_list: true

Induced

name: ParsedPaper
description: 'One paper as text, tables and bibliographic facts. The same shape for
  every download source.

  The text is the only offset space. Every evidence span an extraction record cites,
  every table row''s position and every text-read point addresses `text_sha256`''s
  characters, so a span can be checked by slicing the text, and a span made against
  a different text is detectably wrong.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  header:
    name: header
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ArtifactHeader
    required: true
    inlined: true
  source:
    name: source
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: string
    required: true
    any_of:
    - range: DocumentSource
    - range: string
  source_reason:
    name: source_reason
    description: Why this source's text was chosen over the others downloaded, such
      as "most tables" or "first in download order". Every stage reads this one text,
      so the choice is made once and recorded.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: string
  text_copy:
    name: text_copy
    description: The copy the text was read from. Its licence and access, not the
      paper's licence, decide whether the text may be passed on.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: HeldCopy
    required: true
    inlined: true
  reported_copies:
    name: reported_copies
    description: Copies of the paper that a source lists and that we do not hold,
      each with its own licence. Where an open copy is, when `bibliography.oa_status`
      says one exists.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: ReportedCopy
    multivalued: true
    inlined: true
    inlined_as_list: true
  text_path:
    name: text_path
    description: The text file's path, relative to the paper's bundle directory.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: string
    required: true
  text_sha256:
    name: text_sha256
    description: sha256 of the text file's UTF-8 bytes. This artifact's fingerprint.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: string
    required: true
  text_length:
    name: text_length
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: integer
    minimum_value: 0
  bibliography:
    name: bibliography
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: Bibliography
    required: true
    inlined: true
  is_meta_analysis:
    name: is_meta_analysis
    description: Whether the paper is itself a meta-analysis or review, decided here
      once. Every consumer reads this field; none applies its own test.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: boolean
    required: true
  is_meta_analysis_basis:
    name: is_meta_analysis_basis
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: MetaAnalysisBasis
  sections:
    name: sections
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: Section
    multivalued: true
    inlined: true
    inlined_as_list: true
  supplements:
    name: supplements
    description: Supplementary material the paper links to, and whether it was fetched.
      A result the text cites to a supplement that was not fetched is reported elsewhere,
      not missing.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: Supplement
    multivalued: true
    inlined: true
    inlined_as_list: true
  references:
    name: references
    description: The paper's reference list, in order. Usually fetched from an API
      by the paper's identifiers rather than parsed from the text (`Reference.provider`
      says which), so it is complete and carries DOIs even when the text's list is
      badly extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    - Citation
    range: Reference
    multivalued: true
    inlined: true
    inlined_as_list: true
  citations:
    name: citations
    description: 'Every in-text citation, where it sits in the text and which reference
      it points to. The link from a sentence to a work, which the reference list alone
      cannot give: what resolves the citations a task''s description makes (storage
      `Task.reference_ids`) and traces a task to the paper that introduced it.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    range: Citation
    multivalued: true
    inlined: true
    inlined_as_list: true
  tables:
    name: tables
    from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
    rank: 1000
    owner: ParsedPaper
    domain_of:
    - ParsedPaper
    - CoordinateParse
    range: ParsedTable
    multivalued: true
    inlined: true
    inlined_as_list: true