git.iko.soy/typeable/pandoc
on master help sign in
JATS writer: support author affiliations (#6867)
797db8dAlbert Krewinkel
data/templates/affiliations.jatsnew file+35
compare with master
unifiedsplit
@@ -0,0 +1,35 @@
1+$--
2+$-- Affiliations
3+$--
4+$for(affiliation)$
5+<aff id="aff-$affiliation.id$">
6+$-- wrap affiliation if it has a known institution identifier
7+$if(affiliation.group)$
8+<institution content-type="group">$affiliation.group$</institution>
9+$endif$
10+$if(affiliation.department)$
11+<institution content-type="dept">$affiliation.department$</institution>
12+$endif$
13+<institution-wrap>
14+$if(affiliation.organization)$
15+<institution>$affiliation.organization$</institution>
16+$else$
17+<institution>$affiliation.name$</institution>
18+$endif$
19+$if(affiliation.isni)$
20+<institution-id institution-id-type="ISNI">$affiliation.isni$</institution-id>
21+$endif$
22+$if(affiliation.ringgold)$
23+<institution-id institution-id-type="Ringgold">$affiliation.ringgold$</institution-id>
24+$endif$
25+$if(affiliation.ror)$
26+<institution-id institution-id-type="ROR">$affiliation.ror$</institution-id>
27+$endif$
28+</institution-wrap>$if(affiliation.street-address)$,
29+$for(affiliation.street-address)$
30+<addr-line>$affiliation.street-address$</addr-line>$sep$,
31+$endfor$
32+$else$$if(affiliation.city)$, <city>$affiliation.city$</city>$endif$$endif$$if(affiliation.country)$,
33+<country$if(affiliation.country-code)$ country="$affiliation.country-code$"$endif$>$affiliation.country$</country>$endif$
34+</aff>
35+$endfor$
data/templates/article.jats_publishing+4−3
@@ -101,14 +101,15 @@ $endif$
101$if(author.email)$
101$if(author.email)$
102<email>$author.email$</email>
102<email>$author.email$</email>
103$endif$
103$endif$
104−$if(author.aff-id)$
104+$for(author.affiliation)$
105−<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
105+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
106−$endif$
106+$endfor$
107$if(author.cor-id)$
107$if(author.cor-id)$
108<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
108<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
109$endif$
109$endif$
110</contrib>
110</contrib>
111$endfor$
111$endfor$
112+${ affiliations.jats() }
112</contrib-group>
113</contrib-group>
113$endif$
114$endif$
114$if(article.author-notes)$
115$if(article.author-notes)$
data/templates/default.jats_articleauthoring+4−3
@@ -34,14 +34,15 @@ $endif$
34$if(author.email)$
34$if(author.email)$
35<email>$author.email$</email>
35<email>$author.email$</email>
36$endif$
36$endif$
37−$if(author.aff-id)$
37+$for(author.affiliation)$
38−<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
38+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
39−$endif$
39+$endfor$
40$if(author.cor-id)$
40$if(author.cor-id)$
41<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
41<xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
42$endif$
42$endif$
43</contrib>
43</contrib>
44$endfor$
44$endfor$
45+${ affiliations.jats() }
45</contrib-group>
46</contrib-group>
46$endif$
47$endif$
47$if(copyright)$
48$if(copyright)$
doc/jats.md+84
@@ -39,6 +39,12 @@ Metadata Values
39 Used as the contents of the [`<email>`][elem:given-names]
39 Used as the contents of the [`<email>`][elem:given-names]
40 element.
40 element.
41
41
42+ `affiliation`
43+ : list of affiliation identifiers; marks the organizations
44+ with which an author is affiliated. Each identifier in this
45+ list must also occur as the `id` of an affiliation listed in
46+ the top-level `affiliation` list.
47+
42 `cor-id`
48 `cor-id`
43 : identifier linking to the contributor's correspondence
49 : identifier linking to the contributor's correspondence
44 information. The info itself must be stored in as an item in
50 information. The info itself must be stored in as an item in
@@ -48,6 +54,73 @@ Metadata Values
48 [`rid`][attr:rid] attribute is set to `cor-<ID>`, where
54 [`rid`][attr:rid] attribute is set to `cor-<ID>`, where
49 `<ID>` is the stringified value of this attribute.
55 `<ID>` is the stringified value of this attribute.
50
56
57+`affiliation`
58+: the list of organizations with which contributors are
59+ affiliated. Each institution is added as an [`<aff>`] element to
60+ the author's contrib-group.
61+
62+ The fields are given in the order in which they are included in
63+ the output.
64+
65+ `id`
66+ : internal identifier; used as the [`<aff>`] element's `id`
67+ value, prefixed with `aff-`.
68+
69+ `group`
70+ : name of the research group or other low-level organizational
71+ structure; used as value of an [`<institution>`] element with
72+ [`content-type`][attr:content-type] set to `group`.
73+
74+ `department`
75+ : name of the department or other mid-level organizational
76+ structure; used as value of an [`<institution>`] element with
77+ [`content-type`][attr:content-type] set to `dept`.
78+
79+ `organization`
80+ : name of the company, university, or other top-level
81+ organizational structure; used as value of an
82+ [`<institution>`] element. The institution element is wrapped
83+ in an [`<institution-wrap>`] element; any identifiers, like
84+ `ringgold` or `ror`, are added to the wrapper and must hence
85+ belong to this organization (not the department or group).
86+
87+ `isni`
88+ : International Standard Name Identifier of the organization.
89+ Added via an [`<institution-id>`] element with
90+ [`institution-id-type`](attr:institution-id-type) set to
91+ `ISNI`.
92+
93+ `ringgold`
94+ : [Ringgold] identifier of the organization. Added via an
95+ [`<institution-id>`] element with
96+ [`institution-id-type`](attr:institution-id-type) set to
97+ `Ringgold`.
98+
99+ `ror`
100+ : Research Organization Registry identifier of the
101+ organization. Added via an [`<institution-id>`] element with
102+ [`institution-id-type`](attr:institution-id-type) set to
103+ `ROR`.
104+
105+ `street-address`
106+ : The organization's street address; each list item is wrapped
107+ in an [`<addr-line>`] element, separated by a comma and
108+ space (`, `).
109+
110+ `city`
111+ : City in which the organization is located; used only if
112+ `street-address` is not given, in which case the value is
113+ wrapped in a [`<city>`] element.
114+
115+ `country`
116+ : Country in which the organization is located; used as the
117+ value of a [`<country>`] element.
118+
119+ `country-code`
120+ : Two letter ISO-3166-1 country identifier; used as the
121+ [`country`][attr:country] attribute in element [`<country>`]
122+ (if the latter is present).
123+
51`copyright`
124`copyright`
52: Licensing and copyright information. This information is
125: Licensing and copyright information. This information is
53 rendered via the [`<permissions>`][elem:permissions] element.
126 rendered via the [`<permissions>`][elem:permissions] element.
@@ -258,7 +331,10 @@ Required metadata values:
258 `journal.pmc`.
331 `journal.pmc`.
259- One or more of `journal.pissn`, `journal.eissn`.
332- One or more of `journal.pissn`, `journal.eissn`.
260
333
334+[Ringgold]: https://ringgold.com/
335+[attr:content-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/content-type.html
261[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
336[attr:fn-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/fn-type.html
337+[attr:institution-id-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/institution-id-type.html
262[attr:iso-8601-date]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/iso-8601-date.html
338[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
339[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
340[attr:kwd-group-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/kwd-group-type.html
@@ -297,3 +373,11 @@ Required metadata values:
297[elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.html
373[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
374[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
375[elem:xref]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/xref.html
376+
377+[`<addr-line>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/addr-line.html
378+[`<aff>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/aff.html
379+[`<city>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/city.html
380+[`<country>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/country.html
381+[`<institution-id>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-id.html
382+[`<institution-wrap>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution-wrap.html
383+[`<institution>`]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/institution.html