JATS
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 contributorsstring-name
.orcid
- the contributor’s ORCID identifier.
surname
surname of the contributor. Usually the family name in western names.
See
<surname>
.given-names
personal names of the contributor; this includes middle names (if any) in western-style names.
See
<given-names>
.email
the contributor’s email address.
Used as the contents of the
<email>
element.affiliation
- list of affiliation identifiers; marks 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-levelaffiliation
list. 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 thecor-id
value is then, an<xref>
link ofref-type
corresp
is added. Therid
attribute is set tocor-<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’sid
value, prefixed withaff-
. group
- name of the research group or other low-level organizational structure; used as value of an
<institution>
element withcontent-type
set togroup
. department
- name of the department or other mid-level organizational structure; used as value of an
<institution>
element withcontent-type
set todept
. 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, likeringgold
orror
, 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 withinstitution-id-type
set toISNI
. ringgold
- Ringgold identifier of the organization. Added via an
<institution-id>
element withinstitution-id-type
set toRinggold
. ror
- Research Organization Registry identifier of the organization. Added via an
<institution-id>
element withinstitution-id-type
set toROR
. pid
- Array of persistent identifiers which are added as
<institution-id>
elements. Each item must contain a map with keystype
, used asinstitution-id-type
, andid
, 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
Licensing and copyright information. This information is rendered via the
<permissions>
element.The variables
type
,link
, andtext
should always be used together.statement
- the year of copyright; used as content of the
<copyright-statement>
year
- the year of copyright; used as content of the
<copyright-year>
holder
- the copyright holder; included via the
<copyright-holder>
element. text
- inline text setting the license under which the text is published; included via the
<license-p>
element. type
- type of the license; used as value of the
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. Thepub-type
attribute is always set toepub
.iso-8601
ISO-8601 representation of the publication date. Used as the value of the
pub-date
element’siso-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.
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>
element with attributepub-id-type
set topublisher-id
. doi
- Digital Object Identifier (DOI) assigned to the article. Used as the content of the
<article-id>
element with attributepub-id-type
set todoi
. pmid
- PubMed Identifier (PubMed ID) assigned to the article. Used as the content of the
<article-id>
element with attributepub-id-type
set topmid
. pmcid
- PubMed Central Identifier assigned to the article. Used as the content of the
<article-id>
element with attributepub-id-type
set topmcid
. art-access-id
- generic article accession identifier. Used as the content of the
<article-id>
element with attributepub-id-type
set toart-access-id
. heading
- name of a subject or topic describing the article. Used as the content of the
<subject>
element, nested in a<subj-group>
element which hasheading
as itssubj-group-type
attribute. categories
- list a subject or topic describing the article. Items are each used as the content a the
<subject>
element, grouped in a single<subj-group>
element with itssubj-group-type
attribute set tocategories
. 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>
) offn-type
conflict
. con
- Contributed-by information. Rendered as a footnote (
<fn>
) offn-type
con
. corresp
- Correspondence information. This must be a list of contributor correspondence items, where each item must have the properties
id
andemail
. The info is then rendered via a<corresp>
element.
funding-statement
- Prose describing the funding. Added to the article’s frontmatter via the
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>
with attributejournal-id-type
set topublisher-id
. nlm-ta
- journal identifier assigned by PubMed. Used as content of element
<journal-id>
with attributejournal-id-type
set tonlm-ta
. pmc
- journal identifier assigned by PubMed Central. Used as content of element
<journal-id>
with attributejournal-id-type
set topmc
. title
- full title of the journal in which the article is published. Used as content of the
<journal-title>
element. abbrev-title
- short form of the journal title. Used as content of the
<abbrev-journal-title>
element. pissn
- ISSN identifier of the publication’s print version. Used as content of the
<issn>
element with thepub-type
attribute set toppub
. eissn
- ISSN identifier of the publication’s electronic version. Used as content of the
<issn>
element with thepub-type
attribute set toepub
. publisher-name
- name of the publishing entity (person, company, or other). Used as the content of the
<publisher-name>
element. publisher-loc
- place of publication. Used as the content of the
<publisher-loc>
element.
notes
- Additional notes concerning the whole article. Added to the article’s frontmatter via the
<notes>
element. tags
- list of keywords. Items are used as contents of the
<kwd>
element; the elements are grouped in a<kwd-group>
with thekwd-group-type
valueauthor
.
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
.