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Class: Bibliography

The paper's bibliographic facts, as the metadata lookup returned them. Defined once: the parsed paper carries it, and the storage Study holds the same object as Study.bibliography, so nothing is copied field by field and nothing is extracted.

URI: parse:Bibliography

 classDiagram
    class Bibliography
    click Bibliography href "../Bibliography/"
      Bibliography : abstract

      Bibliography : abstract_provider





        Bibliography --> "0..1" MetadataSource : abstract_provider
        click MetadataSource href "../MetadataSource/"



      Bibliography : authors

      Bibliography : corrections





        Bibliography --> "*" Correction : corrections
        click Correction href "../Correction/"



      Bibliography : issue

      Bibliography : journal

      Bibliography : keywords

      Bibliography : language

      Bibliography : license





        Bibliography --> "1" License : license
        click License href "../License/"



      Bibliography : oa_status





        Bibliography --> "0..1" OaStatus : oa_status
        click OaStatus href "../OaStatus/"



      Bibliography : pages

      Bibliography : provider





        Bibliography --> "0..1" MetadataSource : provider
        click MetadataSource href "../MetadataSource/"



      Bibliography : publication_types

      Bibliography : publication_year

      Bibliography : title

      Bibliography : volume

Slots

Name Cardinality and Range Description Inheritance
title 1
String		 direct
authors *
String		 Author names in published order direct
journal 0..1
String		 direct
publication_year 0..1
Integer		 Year in which the study was first published or made publicly available direct
volume 0..1
String		 direct
issue 0..1
String		 direct
pages 0..1
String		 direct
abstract 0..1
String		 Absent (null) when no source gave one; never an empty string direct
abstract_provider 0..1
MetadataSource		 The source whose abstract abstract is direct
language *
String		 Languages of the article, as the E-utilities API reports them -- the three-le... direct
publication_types *
String or 
StudyType		 PubMed publication types for this record, verbatim as the E-utilities API ret... direct
keywords *
String		 direct
license 1
License		 The paper's licence: the version of record's, or the latest preprint's while ... direct
oa_status 0..1
OaStatus		 direct
corrections *
Correction		 Notices attached to the paper -- errata, retractions, expressions of concern ... direct
provider 0..1
MetadataSource		 The metadata service the facts came from direct

Usages

used by used in type used
ParsedPaper bibliography range Bibliography

Rules

Rule Applied Preconditions Postconditions Elseconditions
slot_conditions {'abstract': {'any_of': [{'range': 'string'}]}} {'abstract_provider': {'value_presence': 'PRESENT', 'any_of': [{'range': 'MetadataSource'}]}} {'abstract_provider': {'none_of': [{'range': 'MetadataSource'}]}}

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Bibliography
description: 'The paper''s bibliographic facts, as the metadata lookup returned them.
  Defined once: the parsed paper carries it, and the storage Study holds the same
  object as `Study.bibliography`, so nothing is copied field by field and nothing
  is extracted.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  title:
    name: title
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    - Reference
    range: string
    required: true
  authors:
    name: authors
    description: Author names in published order.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  journal:
    name: journal
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
  publication_year:
    name: publication_year
    description: Year in which the study was first published or made publicly available.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: integer
    minimum_value: 1600
  volume:
    name: volume
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
  issue:
    name: issue
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
  pages:
    name: pages
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
  abstract:
    name: abstract
    description: Absent (null) when no source gave one; never an empty string.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
    pattern: \S
  abstract_provider:
    name: abstract_provider
    description: The source whose abstract `abstract` is. It may differ from `provider`.
      The abstract is the publisher's abstract of the version `license` describes,
      so its licence is `license`.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: MetadataSource
  language:
    name: language
    description: 'Languages of the article, as the E-utilities API reports them --
      the three-letter codes PubMed assigns, `eng` and the rest, and not read off
      the paper: the text a reader is given is in one language whatever the article
      is indexed as.

      At least six of the benchmark''s sixteen meta-analyses state "English language"
      as an inclusion criterion. On the 1,804 records measured it excludes exactly
      one paper, so it buys precision rather than recall; the criterion is stated,
      so the field states it.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  publication_types:
    name: publication_types
    description: 'PubMed publication types for this record, verbatim as the E-utilities
      API returns them (https://pubmed.ncbi.nlm.nih.gov/help/#publication-types).
      Multivalued because PubMed assigns several: every article is `Journal Article`
      and the design of the study motivates other labels. `StudyType` lists the known
      types only; any other type PubMed returns is kept verbatim.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    multivalued: true
    any_of:
    - range: StudyType
    - range: string
  keywords:
    name: keywords
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  license:
    name: license
    description: 'The paper''s licence: the version of record''s, or the latest preprint''s
      while the header''s `publication_status` is `preprint`. Not the licence of a
      copy of another version, which that copy carries.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    - Copy
    range: License
    required: true
    inlined: true
  oa_status:
    name: oa_status
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: OaStatus
  corrections:
    name: corrections
    description: Notices attached to the paper -- errata, retractions, expressions
      of concern -- as the indexer lists them. A retracted paper is still parsed and
      stored, marked by its `retraction` notice, and left out of studysets by default;
      a filter can ask for it explicitly.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    range: Correction
    multivalued: true
    inlined_as_list: true
  provider:
    name: provider
    description: The metadata service the facts came from.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    domain_of:
    - Bibliography
    - Reference
    range: MetadataSource
rules:
- preconditions:
    slot_conditions:
      abstract:
        name: abstract
        any_of:
        - range: string
  postconditions:
    slot_conditions:
      abstract_provider:
        name: abstract_provider
        value_presence: PRESENT
        any_of:
        - range: MetadataSource
  elseconditions:
    slot_conditions:
      abstract_provider:
        name: abstract_provider
        none_of:
        - range: MetadataSource
  open_world: true
  description: An abstract, and only an abstract, says which source it came from.

Induced

name: Bibliography
description: 'The paper''s bibliographic facts, as the metadata lookup returned them.
  Defined once: the parsed paper carries it, and the storage Study holds the same
  object as `Study.bibliography`, so nothing is copied field by field and nothing
  is extracted.'
from_schema: https://neurostuff.org/schemas/neuroimaging-paper-parse
rank: 1000
attributes:
  title:
    name: title
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    - Reference
    range: string
    required: true
  authors:
    name: authors
    description: Author names in published order.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  journal:
    name: journal
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
  publication_year:
    name: publication_year
    description: Year in which the study was first published or made publicly available.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: integer
    minimum_value: 1600
  volume:
    name: volume
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
  issue:
    name: issue
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
  pages:
    name: pages
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
  abstract:
    name: abstract
    description: Absent (null) when no source gave one; never an empty string.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
    pattern: \S
  abstract_provider:
    name: abstract_provider
    description: The source whose abstract `abstract` is. It may differ from `provider`.
      The abstract is the publisher's abstract of the version `license` describes,
      so its licence is `license`.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: MetadataSource
  language:
    name: language
    description: 'Languages of the article, as the E-utilities API reports them --
      the three-letter codes PubMed assigns, `eng` and the rest, and not read off
      the paper: the text a reader is given is in one language whatever the article
      is indexed as.

      At least six of the benchmark''s sixteen meta-analyses state "English language"
      as an inclusion criterion. On the 1,804 records measured it excludes exactly
      one paper, so it buys precision rather than recall; the criterion is stated,
      so the field states it.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  publication_types:
    name: publication_types
    description: 'PubMed publication types for this record, verbatim as the E-utilities
      API returns them (https://pubmed.ncbi.nlm.nih.gov/help/#publication-types).
      Multivalued because PubMed assigns several: every article is `Journal Article`
      and the design of the study motivates other labels. `StudyType` lists the known
      types only; any other type PubMed returns is kept verbatim.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
    multivalued: true
    any_of:
    - range: StudyType
    - range: string
  keywords:
    name: keywords
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: string
    multivalued: true
  license:
    name: license
    description: 'The paper''s licence: the version of record''s, or the latest preprint''s
      while the header''s `publication_status` is `preprint`. Not the licence of a
      copy of another version, which that copy carries.'
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    - Copy
    range: License
    required: true
    inlined: true
  oa_status:
    name: oa_status
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: OaStatus
  corrections:
    name: corrections
    description: Notices attached to the paper -- errata, retractions, expressions
      of concern -- as the indexer lists them. A retracted paper is still parsed and
      stored, marked by its `retraction` notice, and left out of studysets by default;
      a filter can ask for it explicitly.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    range: Correction
    multivalued: true
    inlined: true
    inlined_as_list: true
  provider:
    name: provider
    description: The metadata service the facts came from.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/bibliography
    rank: 1000
    owner: Bibliography
    domain_of:
    - Bibliography
    - Reference
    range: MetadataSource
rules:
- preconditions:
    slot_conditions:
      abstract:
        name: abstract
        any_of:
        - range: string
  postconditions:
    slot_conditions:
      abstract_provider:
        name: abstract_provider
        value_presence: PRESENT
        any_of:
        - range: MetadataSource
  elseconditions:
    slot_conditions:
      abstract_provider:
        name: abstract_provider
        none_of:
        - range: MetadataSource
  open_world: true
  description: An abstract, and only an abstract, says which source it came from.