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1+---
2+title: JATS
3+author: Albert Krewinkel
4+---
5+
6+This document describes pandoc's handling of JATS.
7+
8+Metadata Values
9+===============
10+
11+`abstract`
12+: Article summary. Added via the document's front matter via the
13+ [`<abstract>`][elem:abstract] element.
14+
15+`author`
16+: list of article contributors. Each author should have a surname
17+ and a given name listed in the entry; if the author has no
18+ `surname` value, then the item will be used as the contributors
19+ [`string-name`][elem:string-name].
20+
21+ `orcid`
22+ : the contributor's ORCID identifier.
23+
24+ `surname`
25+ : surname of the contributor. Usually the family name in
26+ western names.
27+
28+ See [`<surname>`][elem:surname].
29+
30+ `given-names`
31+ : personal names of the contributor; this includes middle
32+ names (if any) in western-style names.
33+
34+ See [`<given-names>`][elem:given-names].
35+
36+ `email`
37+ : the contributor's email address.
38+
39+ Used as the contents of the [`<email>`][elem:given-names]
40+ element.
41+
42+ `cor-id`
43+ : identifier linking to the contributor's correspondence
44+ information. The info itself must be stored in as an item in
45+ `article.author-notes.corresp`. If the `cor-id` value is
46+ then, an [`<xref>`][elem:xref] link of
47+ [`ref-type`][attr:ref-type] `corresp` is added. The
48+ [`rid`][attr:rid] attribute is set to `cor-<ID>`, where
49+ `<ID>` is the stringified value of this attribute.
50+
51+`copyright`
52+: Licensing and copyright information. This information is
53+ rendered via the [`<permissions>`][elem:permissions] element.
54+
55+ The variables `type`, `link`, and `text` should always be used
56+ together.
57+
58+ `statement`
59+ : the year of copyright; used as content of the
60+ [`<copyright-statement>`][elem:copyright-statement]
61+
62+ `year`
63+ : the year of copyright; used as content of the
64+ [`<copyright-year>`][elem:copyright-year]
65+
66+ `holder`
67+ : the copyright holder; included via the
68+ [`<copyright-holder>`][elem:copyright-holder] element.
69+
70+ `text`
71+ : inline text setting the license under which the text is
72+ published; included via the
73+ [`<license-p>`][elem:copyright-holder] element.
74+
75+ `type`
76+ : type of the license; used as value of the
77+ [`license-type`][attr:license-type] attribute.
78+
79+ `link`
80+ : external link describing the license; used as value of a
81+ `xlink:href` attribute in the `<license>` element.
82+
83+`date`
84+: publication date. This value should usually be a string
85+ representation of a date. Pandoc will parse and deconstruct the
86+ date into the components given below. It is also possible to
87+ pass these components directly.
88+
89+ The publication date is recorded in the document via the
90+ [`<pub-date>`][elem:pub-date] element and its sub-elements. The
91+ [`pub-type`][attr:pub-type] attribute is always set to `epub`.
92+
93+ `iso-8601`
94+ : ISO-8601 representation of the publication date. Used as the
95+ value of the [`pub-date`][elem:pub-date] element's
96+ [`iso-8601-date`][attr:iso-8601-date] attribute.
97+
98+ This value is set automatically if pandoc can parse the
99+ `date` value as a date.
100+
101+ `day`, `month`, `year`
102+ : Day, month, and year of the publication date. Only the
103+ publication year is required. The values are used as the
104+ contents of the elements with the respective names.
105+
106+ The values are set automatically if pandoc can parse the
107+ `date` value as a date.
108+
109+`article`
110+: information concerning the article that identifies or describes
111+ it. The key-value pairs within this map are typically used
112+ within the [`<article-meta>`][elem:article-meta] element.
113+
114+ `publisher-id`
115+ : external article identifier assigned by the publisher. Used
116+ as the content of the [`<article-id>`][elem:article-id]
117+ element with attribute [`pub-id-type`][attr:pub-id-type] set
118+ to `publisher-id`.
119+
120+ `doi`
121+ : Digital Object Identifier (DOI) assigned to the article.
122+ Used as the content of the [`<article-id>`][elem:article-id]
123+ element with attribute [`pub-id-type`][attr:pub-id-type] set
124+ to `doi`.
125+
126+ `pmid`
127+ : PubMed Identifier (PubMed ID) assigned to the article. Used
128+ as the content of the [`<article-id>`][elem:article-id]
129+ element with attribute [`pub-id-type`][attr:pub-id-type] set
130+ to `pmid`.
131+
132+ `pmcid`
133+ : PubMed Central Identifier assigned to the article. Used as
134+ the content of the [`<article-id>`][elem:article-id] element
135+ with attribute [`pub-id-type`][attr:pub-id-type] set to
136+ `pmcid`.
137+
138+ `art-access-id`
139+ : generic article accession identifier. Used as the content of
140+ the [`<article-id>`][elem:article-id] element with attribute
141+ [`pub-id-type`][attr:pub-id-type] set to `art-access-id`.
142+
143+ `heading`
144+ : name of a subject or topic describing the article. Used as
145+ the content of the [`<subject>`][elem:subject] element,
146+ nested in a [`<subj-group>`][elem:subj-group] element which
147+ has `heading` as its
148+ [`subj-group-type`][attr:subj-group-type] attribute.
149+
150+ `categories`
151+ : list a subject or topic describing the article. Items are
152+ each used as the content a the [`<subject>`][elem:subject]
153+ element, grouped in a single
154+ [`<subj-group>`][elem:subj-group] element with its
155+ [`subj-group-type`][attr:subj-group-type] attribute set to
156+ `categories`.
157+
158+ `author-notes`
159+ : Additional information about authors, like conflict of
160+ interest statements and corresponding author contact info.
161+ Wrapped in an [`<author-notes>`][elem:author-notes] element.
162+
163+ `conflict`
164+ : Conflict of interest statement. Rendered as a footnote
165+ ([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type)
166+ `conflict`.
167+
168+ `con`
169+ : Contributed-by information. Rendered as a footnote
170+ ([`<fn>`][elem:fn]) of [`fn-type`](attr:fn-type) `con`.
171+
172+ `corresp`
173+ : Correspondence information. This must be a list of
174+ contributor correspondence items, where each item must
175+ have the properties `id` and `email`. The info is then
176+ rendered via a [`<corresp>`][elem:corresp] element.
177+
178+ `funding-statement`
179+ : Prose describing the funding. Added to the article's
180+ frontmatter via the
181+ [`funding-statement`][elem:funding-statement] element.
182+
183+`journal`
184+: information on the journal in which the article is published.
185+ This must be a map; the following key/value pairs are
186+ recognized.
187+
188+ `publisher-id`
189+ : journal identifier assigned by the publisher. Used as
190+ content of element [`<journal-id>`][elem:journal-id] with
191+ attribute [`journal-id-type`][attr:journal-id-type] set to
192+ `publisher-id`.
193+
194+ `nlm-ta`
195+ : journal identifier assigned by PubMed. Used as content of
196+ element [`<journal-id>`][elem:journal-id] with attribute
197+ [`journal-id-type`][attr:journal-id-type] set to `nlm-ta`.
198+
199+ `pmc`
200+ : journal identifier assigned by PubMed Central. Used as
201+ content of element [`<journal-id>`][elem:journal-id] with
202+ attribute [`journal-id-type`][attr:journal-id-type] set to
203+ `pmc`.
204+
205+ `title`
206+ : full title of the journal in which the article is published.
207+ Used as content of the
208+ [`<journal-title>`][elem:journal-title] element.
209+
210+ `abbrev-title`
211+ : short form of the journal title. Used as content of the
212+ [`<abbrev-journal-title>`][elem:abbrev-journal-title]
213+ element.
214+
215+ `pissn`
216+ : ISSN identifier of the publication's print version. Used as
217+ content of the [`<issn>`][elem:issn] element with the
218+ [`pub-type`][attr:pub-type] attribute set to `ppub`.
219+
220+ `eissn`
221+ : ISSN identifier of the publication's electronic version.
222+ Used as content of the [`<issn>`][elem:issn] element with
223+ the [`pub-type`][attr:pub-type] attribute set to `epub`.
224+
225+ `publisher-name`
226+ : name of the publishing entity (person, company, or other).
227+ Used as the content of the
228+ [`<publisher-name>`][elem:publisher-name] element.
229+
230+ `publisher-loc`
231+ : place of publication. Used as the content of the
232+ [`<publisher-loc>`][elem:publisher-loc] element.
233+
234+`notes`
235+: Additional notes concerning the whole article. Added to the
236+ article's frontmatter via the [`<notes>`][elem:notes] element.
237+
238+`tags`
239+: list of keywords. Items are used as contents of the
240+ [`<kwd>`][elem:kwd] element; the elements are grouped in a
241+ [`<kwd-group>`][elem:kwd-group] with the
242+ [`kwd-group-type`][attr:kwd-group-type] value `author`.
243+
244+Required Metadata
245+-----------------
246+
247+Pandoc will try to generate a valid JATS document even when
248+information is missing, filling in placeholders or using empty
249+values. This circumvents the intend to ensure a minimum set of
250+information being present in documents of a certain tag set. It is
251+hence recommended to always provide the information listed below.
252+
253+### Publishing Tag Set
254+
255+Required metadata values:
256+
257+- One or more of `journal.publisher-id`, `journal.nlm-ta`,
258+ `journal.pmc`.
259+- One or more of `journal.pissn`, `journal.eissn`.
260+
261+[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
262+[attr:iso-8601-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/iso-8601-date.html
263+[attr:journal-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/journal-id-type.html
264+[attr:kwd-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/kwd-group-type.html
265+[attr:license-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/license-type.html
266+[attr:pub-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/pub-id-type.html
267+[attr:pub-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/pub-type.html
268+[attr:ref-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/ref-type.html
269+[attr:rid]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/rid.html
270+[attr:subj-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/subj-group-type.html
271+[elem:abbrev-journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abbrev-journal-title.html
272+[elem:abstract]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/abstract.html
273+[elem:article-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-id.html
274+[elem:article-meta]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/article-meta.html
275+[elem:copyright-holder]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-holder.html
276+[elem:copyright-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-statement.html
277+[elem:copyright-year]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/copyright-year.html
278+[elem:corresp]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/corresp.html
279+[elem:email]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/email.html
280+[elem:fn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/fn.html
281+[elem:funding-statement]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/funding-statement.html
282+[elem:given-names]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/given-names.html
283+[elem:issn]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/issn.html
284+[elem:journal-id]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-id.html
285+[elem:journal-title]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/journal-title.html
286+[elem:kwd-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd-group.html
287+[elem:kwd]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/kwd.html
288+[elem:license-p]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license-p.html
289+[elem:license]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/license.html
290+[elem:notes]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/notes.html
291+[elem:permissions]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/permissions.html
292+[elem:pub-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/pub-date.html
293+[elem:publisher-loc]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-loc.html
294+[elem:publisher-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/publisher-name.html
295+[elem:string-name]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/string-name.html
296+[elem:subj-group]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subj-group.html
297+[elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.html
298+[elem:surname]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/surname.html
299+[elem:xref]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/xref.html