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This document describes pandoc's handling of JATS.

Metadata Values

abstract : Article summary. Added via the document's front matter via the <abstract> element.

author : list of article contributors. Each author should have a surname and a given name listed in the entry; if the author has no surname value, then the item will be used as the contributors string-name.

`orcid`
:   the contributor's ORCID identifier.

`surname`
:   surname of the contributor. Usually the family name in
    western names.

    See [`<surname>`][elem:surname].

`given-names`
:   personal names of the contributor; this includes middle
    names (if any) in western-style names.

    See [`<given-names>`][elem:given-names].

`name`
:   full name of the author; included only as a fallback if
    `author.surname` is not available. Tagged with
    [`<string-name>`][elem:string-name].

`email`
:   the contributor's email address.

    Used as the contents of the [`<email>`][elem:given-names]
    element.

`affiliation`
:   either full affiliation entries as described in field
    `affiliation`, or a list of affiliation identifiers.

    The identifiers link to the organizations with which an
    author is affiliated. Each identifier in this list must
    also occur as the `id` of an affiliation listed in the
    top-level `affiliation` list.

    If the top-level `affiliation` field is set, then this
    entry assumed to be a list of identifiers, and a list of
    full entries if that field is unset.

    Full entries must be given if the articleauthoring tag
    set it used, as affiliation links are not allowed in that
    schema.

`equal-contrib`
:   boolean attribute used to mark authors who contributed
    equally to the work. The
    [`equal-contrib`][attr:equal-contrib] attribute, set to
    `yes`, is added to the author's [`<contrib>`] element if
    this is set to a truthy value.

`cor-id`
:   identifier linking to the contributor's correspondence
    information. The info itself must be stored in as an item in
    `article.author-notes.corresp`. If the `cor-id` value is
    then, an [`<xref>`][elem:xref] link of
    [`ref-type`][attr:ref-type] `corresp` is added. The
    [`rid`][attr:rid] attribute is set to `cor-<ID>`, where
    `<ID>` is the stringified value of this attribute.

affiliation : the list of organizations with which contributors are affiliated. Each institution is added as an <aff> element to the author's contrib-group.

The fields are given in the order in which they are included in
the output.

`id`
:   internal identifier; used as the [`<aff>`] element's `id`
    value, prefixed with `aff-`.

`group`
:   name of the research group or other low-level organizational
    structure; used as value of an [`<institution>`] element with
    [`content-type`][attr:content-type] set to `group`.

`department`
:   name of the department or other mid-level organizational
    structure; used as value of an [`<institution>`] element with
    [`content-type`][attr:content-type] set to `dept`.

`organization`
:   name of the company, university, or other top-level
    organizational structure; used as value of an
    [`<institution>`] element. The institution element is wrapped
    in an [`<institution-wrap>`] element; any identifiers, like
    `ringgold` or `ror`, are added to the wrapper and must hence
    belong to this organization (not the department or group).

`isni`
:   International Standard Name Identifier of the organization.
    Added via an [`<institution-id>`] element with
    [`institution-id-type`](attr:institution-id-type) set to
    `ISNI`.

`ringgold`
:   [Ringgold] identifier of the organization. Added via an
    [`<institution-id>`] element with
    [`institution-id-type`](attr:institution-id-type) set to
    `Ringgold`.

`ror`
:   Research Organization Registry identifier of the
    organization. Added via an [`<institution-id>`] element with
    [`institution-id-type`](attr:institution-id-type) set to
    `ROR`.

`pid`
:   Array of persistent identifiers which are added as
    [`<institution-id>`] elements. Each item must contain a map
    with keys `type`, used as
    [`institution-id-type`](attr:institution-id-type), and `id`,
    used as element content.

`street-address`
:   The organization's street address; each list item is wrapped
    in an [`<addr-line>`] element, separated by a comma and
    space (`, `).

`city`
:   City in which the organization is located; used only if
    `street-address` is not given, in which case the value is
    wrapped in a [`<city>`] element.

`country`
:   Country in which the organization is located; used as the
    value of a [`<country>`] element.

`country-code`
:   Two letter ISO-3166-1 country identifier; used as the
    [`country`][attr:country] attribute in element [`<country>`]
    (if the latter is present).

copyright : Copyright and licensing information. This information is rendered via the <permissions> element.

It is recommended to use the `license` field (described below)
for licensing information. If licensing information is
included below `copyright`, then the variables `type`, `link`,
and `text` should always be used together.

`statement`
:   copyright notice or statement; used as content of the
    [`<copyright-statement>`][elem:copyright-statement]. Use a
    list for multiple statements.

`year`
:   the year of copyright; used as content of the
    [`<copyright-year>`][elem:copyright-year]. Use a list to
    for multiple copyright years. The JATS documentation
    states that this field need not to be used if the year is
    included in the copyright statement.

`holder`
:   the copyright holder; included via the
    [`<copyright-holder>`][elem:copyright-holder] element. Use
    a list for multiple copyright holders.

`text`
:   inline text setting the license under which the text is
    published; included via the
    [`<license-p>`][elem:copyright-holder] element.

`type`
:   type of the license; used as value of the
    [`license-type`][attr:license-type] attribute.

`link`
:   external link describing the license; used as value of a
    `xlink:href` attribute in the `<license>` element.

date : publication date. This value should usually be a string representation of a date. Pandoc will parse and deconstruct the date into the components given below. It is also possible to pass these components directly.

The publication date is recorded in the document via the
[`<pub-date>`] element and its sub-elements. The
[`publication-format`][attr:publication-format] attribute is
always set to `electronic`.

`iso-8601`
:   ISO-8601 representation of the publication date. Used as the
    value of the [`<pub-date>`] element's
    [`iso-8601-date`][attr:iso-8601-date] attribute.

    This value is set automatically if pandoc can parse the
    `date` value as a date.

`day`, `month`, `year`
:   Day, month, and year of the publication date. Only the
    publication year is required. The values are used as the
    contents of the elements with the respective names.

    The values are set automatically if pandoc can parse the
    `date` value as a date.

`type`
:   The type of event marked by this date. The value is set as
    the [`date-type`][attr:date-type] attribute on the
    [`<pub-date>`] element and defaults to "pub" if not
    specified.

article : information concerning the article that identifies or describes it. The key-value pairs within this map are typically used within the <article-meta> element.

`publisher-id`
:   external article identifier assigned by the publisher. Used
    as the content of the [`<article-id>`][elem:article-id]
    element with attribute [`pub-id-type`][attr:pub-id-type] set
    to `publisher-id`.

`doi`
:   Digital Object Identifier (DOI) assigned to the article.
    Used as the content of the [`<article-id>`][elem:article-id]
    element with attribute [`pub-id-type`][attr:pub-id-type] set
    to `doi`.

`pmid`
:   PubMed Identifier (PubMed ID) assigned to the article. Used
    as the content of the [`<article-id>`][elem:article-id]
    element with attribute [`pub-id-type`][attr:pub-id-type] set
    to `pmid`.

`pmcid`
:   PubMed Central Identifier assigned to the article. Used as
    the content of the [`<article-id>`][elem:article-id] element
    with attribute [`pub-id-type`][attr:pub-id-type] set to
    `pmcid`.

`art-access-id`
:   generic article accession identifier. Used as the content of
    the [`<article-id>`][elem:article-id] element with attribute
    [`pub-id-type`][attr:pub-id-type] set to `art-access-id`.

`heading`
:   name of a subject or topic describing the article. Used as
    the content of the [`<subject>`][elem:subject] element,
    nested in a [`<subj-group>`][elem:subj-group] element which
    has `heading` as its
    [`subj-group-type`][attr:subj-group-type] attribute.

`categories`
:   list a subject or topic describing the article. Items are
    each used as the content a the [`<subject>`][elem:subject]
    element, grouped in a single
    [`<subj-group>`][elem:subj-group] element with its
    [`subj-group-type`][attr:subj-group-type] attribute set to
    `categories`.

`author-notes`
:   Additional information about authors, like conflict of
    interest statements and corresponding author contact info.
    Wrapped in an [`<author-notes>`][elem:author-notes] element.

    `conflict`
    :   Conflict of interest statement. Rendered as a footnote
        ([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type)
        `conflict`.

    `con`
    :   Contributed-by information. Rendered as a footnote
        ([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type) `con`.

    `corresp`
    :   Correspondence information. This must be a list of
        contributor correspondence items, where each item must
        have the properties `id` and `email`. The info is then
        rendered via a [`<corresp>`][elem:corresp] element.

`funding-statement`
:   Prose describing the funding. Added to the article's
    frontmatter via the
    [`funding-statement`][elem:funding-statement] element.

journal : information on the journal in which the article is published. This must be a map; the following key/value pairs are recognized.

`publisher-id`
:   journal identifier assigned by the publisher. Used as
    content of element [`<journal-id>`][elem:journal-id] with
    attribute [`journal-id-type`][attr:journal-id-type] set to
    `publisher-id`.

`nlm-ta`
:   journal identifier assigned by PubMed. Used as content of
    element [`<journal-id>`][elem:journal-id] with attribute
    [`journal-id-type`][attr:journal-id-type] set to `nlm-ta`.

`pmc`
:   journal identifier assigned by PubMed Central. Used as
    content of element [`<journal-id>`][elem:journal-id] with
    attribute [`journal-id-type`][attr:journal-id-type] set to
    `pmc`.

`title`
:   full title of the journal in which the article is published.
    Used as content of the
    [`<journal-title>`][elem:journal-title] element.

`abbrev-title`
:   short form of the journal title. Used as content of the
    [`<abbrev-journal-title>`][elem:abbrev-journal-title]
    element.

`pissn`
:   ISSN identifier of the publication's print version. Used as
    content of the [`<issn>`][elem:issn] element with the
    [`publication-format`][attr:publication-format] attribute
    set to `print`.

`eissn`
:   ISSN identifier of the publication's electronic version.
    Used as content of the [`<issn>`][elem:issn] element with
    the [`publication-format`][attr:publication-format]
    attribute set to `electronic`.

`publisher-name`
:   name of the publishing entity (person, company, or other).
    Used as the content of the
    [`<publisher-name>`][elem:publisher-name] element.

`publisher-loc`
:   place of publication. Used as the content of the
    [`<publisher-loc>`][elem:publisher-loc] element.

license : Article licensing information. Each item of this field is rendered as a <license> element within the <permissions> element.

Item content should be either a single paragraph, or a map
with the fields listed below.

`text`
:   inline text describing a license under which the text is
    published; included via the
    [`<license-p>`][elem:copyright-holder] element.

`type`
:   type of the license; used as value of the
    [`license-type`][attr:license-type] attribute.

`link`
:   external link describing the license; used as value of a
    `xlink:href` attribute in the `<license>` element.

notes : Additional notes concerning the whole article. Added to the article's frontmatter via the <notes> element.

subtitle : Subordinate part of the document title. Added to the document's front matter as a <subtitle> element.

tags : list of keywords. Items are used as contents of the <kwd> element; the elements are grouped in a <kwd-group> with the kwd-group-type value author.

title : The article title. Added to the document's front matter via the <article-title> element.

Required Metadata

Pandoc will try to generate a valid JATS document even when information is missing, filling in placeholders or using empty values. This circumvents the intend to ensure a minimum set of information being present in documents of a certain tag set. It is hence recommended to always provide the information listed below.

Publishing Tag Set

Required metadata values: