JATS

Metadata Values
- Required Metadata
  - Publishing Tag Set

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>.

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-level affiliation 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 the cor-id value is then, an <xref> link of ref-type corresp is added. The 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 set to group.
department: name of the department or other mid-level organizational structure; used as value of an <institution> element with 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 set to ISNI.
ringgold: Ringgold identifier of the organization. Added via an <institution-id> element with institution-id-type set to Ringgold.
ror: Research Organization Registry identifier of the organization. Added via an <institution-id> element with 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, 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

Licensing and copyright information. This information is rendered via the <permissions> element.

The variables type, link, and text 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. The pub-type attribute is always set to epub.

iso-8601

ISO-8601 representation of the publication date. Used as the value of the pub-date element’s 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.

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 attribute pub-id-type set to publisher-id.

doi

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

pmid

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

pmcid

PubMed Central Identifier assigned to the article. Used as the content of the <article-id> element with attribute pub-id-type set to pmcid.

art-access-id

generic article accession identifier. Used as the content of the <article-id> element with attribute 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> element, nested in a <subj-group> element which has heading as its subj-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 its 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>) of fn-type conflict.
con: Contributed-by information. Rendered as a footnote (<fn>) of 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> 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 attribute journal-id-type set to publisher-id.
nlm-ta: journal identifier assigned by PubMed. Used as content of element <journal-id> with attribute journal-id-type set to nlm-ta.
pmc: journal identifier assigned by PubMed Central. Used as content of element <journal-id> with attribute 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> 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 the pub-type attribute set to ppub.
eissn: ISSN identifier of the publication’s electronic version. Used as content of the <issn> element with the pub-type attribute set to epub.
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 the kwd-group-type value author.

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.