300 lines
13 KiB
Markdown
300 lines
13 KiB
Markdown
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---
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title: JATS
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author: Albert Krewinkel
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---
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This document describes pandoc's handling of JATS.
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Metadata Values
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===============
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`abstract`
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: Article summary. Added via the document's front matter via the
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[`<abstract>`][elem:abstract] element.
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`author`
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: list of article contributors. Each author should have a surname
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and a given name listed in the entry; if the author has no
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`surname` value, then the item will be used as the contributors
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[`string-name`][elem:string-name].
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`orcid`
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: the contributor's ORCID identifier.
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`surname`
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: surname of the contributor. Usually the family name in
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western names.
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See [`<surname>`][elem:surname].
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`given-names`
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: personal names of the contributor; this includes middle
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names (if any) in western-style names.
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See [`<given-names>`][elem:given-names].
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`email`
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: the contributor's email address.
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Used as the contents of the [`<email>`][elem:given-names]
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element.
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`cor-id`
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: identifier linking to the contributor's correspondence
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information. The info itself must be stored in as an item in
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`article.author-notes.corresp`. If the `cor-id` value is
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then, an [`<xref>`][elem:xref] link of
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[`ref-type`][attr:ref-type] `corresp` is added. The
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[`rid`][attr:rid] attribute is set to `cor-<ID>`, where
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`<ID>` is the stringified value of this attribute.
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`copyright`
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: Licensing and copyright information. This information is
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rendered via the [`<permissions>`][elem:permissions] element.
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The variables `type`, `link`, and `text` should always be used
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together.
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`statement`
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: the year of copyright; used as content of the
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[`<copyright-statement>`][elem:copyright-statement]
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`year`
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: the year of copyright; used as content of the
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[`<copyright-year>`][elem:copyright-year]
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`holder`
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: the copyright holder; included via the
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[`<copyright-holder>`][elem:copyright-holder] element.
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`text`
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: inline text setting the license under which the text is
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published; included via the
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[`<license-p>`][elem:copyright-holder] element.
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`type`
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: type of the license; used as value of the
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[`license-type`][attr:license-type] attribute.
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`link`
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: external link describing the license; used as value of a
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`xlink:href` attribute in the `<license>` element.
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`date`
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: publication date. This value should usually be a string
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representation of a date. Pandoc will parse and deconstruct the
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date into the components given below. It is also possible to
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pass these components directly.
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The publication date is recorded in the document via the
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[`<pub-date>`][elem:pub-date] element and its sub-elements. The
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[`pub-type`][attr:pub-type] attribute is always set to `epub`.
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`iso-8601`
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: ISO-8601 representation of the publication date. Used as the
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value of the [`pub-date`][elem:pub-date] element's
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[`iso-8601-date`][attr:iso-8601-date] attribute.
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This value is set automatically if pandoc can parse the
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`date` value as a date.
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`day`, `month`, `year`
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: Day, month, and year of the publication date. Only the
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publication year is required. The values are used as the
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contents of the elements with the respective names.
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The values are set automatically if pandoc can parse the
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`date` value as a date.
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`article`
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: information concerning the article that identifies or describes
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it. The key-value pairs within this map are typically used
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within the [`<article-meta>`][elem:article-meta] element.
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`publisher-id`
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: external article identifier assigned by the publisher. Used
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as the content of the [`<article-id>`][elem:article-id]
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element with attribute [`pub-id-type`][attr:pub-id-type] set
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to `publisher-id`.
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`doi`
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: Digital Object Identifier (DOI) assigned to the article.
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Used as the content of the [`<article-id>`][elem:article-id]
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element with attribute [`pub-id-type`][attr:pub-id-type] set
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to `doi`.
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`pmid`
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: PubMed Identifier (PubMed ID) assigned to the article. Used
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as the content of the [`<article-id>`][elem:article-id]
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element with attribute [`pub-id-type`][attr:pub-id-type] set
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to `pmid`.
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`pmcid`
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: PubMed Central Identifier assigned to the article. Used as
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the content of the [`<article-id>`][elem:article-id] element
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with attribute [`pub-id-type`][attr:pub-id-type] set to
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`pmcid`.
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`art-access-id`
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: generic article accession identifier. Used as the content of
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the [`<article-id>`][elem:article-id] element with attribute
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[`pub-id-type`][attr:pub-id-type] set to `art-access-id`.
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`heading`
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: name of a subject or topic describing the article. Used as
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the content of the [`<subject>`][elem:subject] element,
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nested in a [`<subj-group>`][elem:subj-group] element which
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has `heading` as its
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[`subj-group-type`][attr:subj-group-type] attribute.
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`categories`
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: list a subject or topic describing the article. Items are
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each used as the content a the [`<subject>`][elem:subject]
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element, grouped in a single
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[`<subj-group>`][elem:subj-group] element with its
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[`subj-group-type`][attr:subj-group-type] attribute set to
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`categories`.
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`author-notes`
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: Additional information about authors, like conflict of
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interest statements and corresponding author contact info.
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Wrapped in an [`<author-notes>`][elem:author-notes] element.
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`conflict`
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: Conflict of interest statement. Rendered as a footnote
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([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type)
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`conflict`.
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`con`
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: Contributed-by information. Rendered as a footnote
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([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type) `con`.
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`corresp`
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: Correspondence information. This must be a list of
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contributor correspondence items, where each item must
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have the properties `id` and `email`. The info is then
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rendered via a [`<corresp>`][elem:corresp] element.
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`funding-statement`
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: Prose describing the funding. Added to the article's
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frontmatter via the
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[`funding-statement`][elem:funding-statement] element.
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`journal`
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: information on the journal in which the article is published.
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This must be a map; the following key/value pairs are
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recognized.
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`publisher-id`
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: journal identifier assigned by the publisher. Used as
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content of element [`<journal-id>`][elem:journal-id] with
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attribute [`journal-id-type`][attr:journal-id-type] set to
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`publisher-id`.
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`nlm-ta`
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: journal identifier assigned by PubMed. Used as content of
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element [`<journal-id>`][elem:journal-id] with attribute
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[`journal-id-type`][attr:journal-id-type] set to `nlm-ta`.
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`pmc`
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: journal identifier assigned by PubMed Central. Used as
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content of element [`<journal-id>`][elem:journal-id] with
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attribute [`journal-id-type`][attr:journal-id-type] set to
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`pmc`.
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`title`
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: full title of the journal in which the article is published.
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Used as content of the
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[`<journal-title>`][elem:journal-title] element.
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`abbrev-title`
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: short form of the journal title. Used as content of the
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[`<abbrev-journal-title>`][elem:abbrev-journal-title]
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element.
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`pissn`
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: ISSN identifier of the publication's print version. Used as
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content of the [`<issn>`][elem:issn] element with the
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[`pub-type`][attr:pub-type] attribute set to `ppub`.
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`eissn`
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: ISSN identifier of the publication's electronic version.
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Used as content of the [`<issn>`][elem:issn] element with
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the [`pub-type`][attr:pub-type] attribute set to `epub`.
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`publisher-name`
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: name of the publishing entity (person, company, or other).
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Used as the content of the
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[`<publisher-name>`][elem:publisher-name] element.
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`publisher-loc`
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: place of publication. Used as the content of the
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[`<publisher-loc>`][elem:publisher-loc] element.
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`notes`
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: Additional notes concerning the whole article. Added to the
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article's frontmatter via the [`<notes>`][elem:notes] element.
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`tags`
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: list of keywords. Items are used as contents of the
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[`<kwd>`][elem:kwd] element; the elements are grouped in a
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[`<kwd-group>`][elem:kwd-group] with the
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[`kwd-group-type`][attr:kwd-group-type] value `author`.
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Required Metadata
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-----------------
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Pandoc will try to generate a valid JATS document even when
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information is missing, filling in placeholders or using empty
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values. This circumvents the intend to ensure a minimum set of
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information being present in documents of a certain tag set. It is
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hence recommended to always provide the information listed below.
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### Publishing Tag Set
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Required metadata values:
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- One or more of `journal.publisher-id`, `journal.nlm-ta`,
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`journal.pmc`.
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- One or more of `journal.pissn`, `journal.eissn`.
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[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
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[attr:iso-8601-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/iso-8601-date.html
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[attr:journal-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/journal-id-type.html
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[attr:kwd-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/kwd-group-type.html
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[attr:license-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/license-type.html
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[attr:pub-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/pub-id-type.html
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[attr:pub-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/pub-type.html
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[attr:ref-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/ref-type.html
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[attr:rid]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/rid.html
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[attr:subj-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/subj-group-type.html
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[elem:abbrev-journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abbrev-journal-title.html
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[elem:abstract]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abstract.html
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[elem:article-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-id.html
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[elem:article-meta]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-meta.html
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[elem:copyright-holder]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-holder.html
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[elem:copyright-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-statement.html
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[elem:copyright-year]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-year.html
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[elem:corresp]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/corresp.html
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[elem:email]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/email.html
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[elem:fn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/fn.html
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[elem:funding-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/funding-statement.html
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[elem:given-names]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/given-names.html
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[elem:issn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/issn.html
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[elem:journal-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-id.html
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[elem:journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-title.html
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[elem:kwd-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd-group.html
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[elem:kwd]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd.html
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[elem:license-p]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license-p.html
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[elem:license]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license.html
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[elem:notes]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/notes.html
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[elem:permissions]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/permissions.html
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[elem:pub-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/pub-date.html
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[elem:publisher-loc]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-loc.html
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[elem:publisher-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-name.html
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[elem:string-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/string-name.html
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[elem:subj-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subj-group.html
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[elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.html
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[elem:surname]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/surname.html
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[elem:xref]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/xref.html
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