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pandoc/doc/jats.md
Albert Krewinkel 41af476a3d
JATS template: mark authors with cor-id as corresponding authors 
Corresponding authors are marked by setting the attribute
`corresp="yes"` in their respective `<contrib>` element.
2022-06-24 15:44:38 +02:00

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---
title: JATS
author: Albert Krewinkel
---
This document describes pandoc's handling of [JATS].
Metadata Values
===============
`abstract`
: Article summary. Added via the document's front matter via the
[`<abstract>`][elem: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`][elem: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 as an item in
`article.author-notes.corresp`. If the `cor-id` value is
set, 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.
Furthermore, the [`corresp`][attr:corresp] attribute on
the author's [`<contrib>`] element is set to `yes` if
this attribute is set to a truty.
`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>`][elem: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>`][elem: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>`][elem: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>`][elem:notes] element.
`subtitle`
: Subordinate part of the document title. Added to the
document's front matter as a
[`<subtitle>`][elem:article-title] element.
`tags`
: list of keywords. Items are used as contents of the
[`<kwd>`][elem:kwd] element; the elements are grouped in a
[`<kwd-group>`][elem:kwd-group] with the
[`kwd-group-type`][attr:kwd-group-type] value `author`.
`title`
: The article title. Added to the document's front matter via the
[`<article-title>`][elem: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:
- One or more of `journal.publisher-id`, `journal.nlm-ta`,
`journal.pmc`.
- One or more of `journal.pissn`, `journal.eissn`.
[JATS]: https://jats.nlm.nih.gov/
[Ringgold]: https://ringgold.com/
[attr:content-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/content-type.html
[attr:corresp]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/corresp.html
[attr:date-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/date-type.html
[attr:equal-contrib]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/equal-contrib.html
[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
[attr:institution-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/institution-id-type.html
[attr:iso-8601-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/iso-8601-date.html
[attr:journal-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/journal-id-type.html
[attr:kwd-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/kwd-group-type.html
[attr:license-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/license-type.html
[attr:pub-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/pub-id-type.html
[attr:publication-format]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/publication-format.html
[attr:ref-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/ref-type.html
[attr:rid]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/rid.html
[attr:subj-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/subj-group-type.html
[elem:abbrev-journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abbrev-journal-title.html
[elem:abstract]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abstract.html
[elem:article-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-id.html
[elem:article-meta]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-meta.html
[elem:article-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-title.html
[elem:copyright-holder]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-holder.html
[elem:copyright-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-statement.html
[elem:copyright-year]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-year.html
[elem:corresp]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/corresp.html
[elem:email]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/email.html
[elem:fn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/fn.html
[elem:funding-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/funding-statement.html
[elem:given-names]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/given-names.html
[elem:issn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/issn.html
[elem:journal-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-id.html
[elem:journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-title.html
[elem:kwd-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd-group.html
[elem:kwd]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd.html
[elem:license-p]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license-p.html
[elem:license]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license.html
[elem:notes]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/notes.html
[elem:permissions]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/permissions.html
[elem:publisher-loc]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-loc.html
[elem:publisher-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-name.html
[elem:string-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/string-name.html
[elem:subj-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subj-group.html
[elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.html
[elem:subtitle]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subtitle.html
[elem:surname]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/surname.html
[elem:xref]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/xref.html
[`<addr-line>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/addr-line.html
[`<aff>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/aff.html
[`<city>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/city.html
[`<contrib>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/contrib.html
[`<country>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/country.html
[`<institution-id>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-id.html
[`<institution-wrap>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-wrap.html
[`<institution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution.html
[`<pub-date>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/pub-date.html
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