JATS writer: support author affiliations (#6867)

Closes: #6687
2020-11-20 18:57:06 +01:00 · 2020-11-20 18:57:06 +01:00 · 797db8d306
commit 797db8d306
parent c647948ff1
4 changed files with 127 additions and 6 deletions
--- a/data/templates/affiliations.jats
+++ b/data/templates/affiliations.jats
@ -0,0 +1,35 @@
+$--
+$-- Affiliations
+$--
+$for(affiliation)$
+<aff id="aff-$affiliation.id$">
+$-- wrap affiliation if it has a known institution identifier
+$if(affiliation.group)$
+<institution content-type="group">$affiliation.group$</institution>
+$endif$
+$if(affiliation.department)$
+<institution content-type="dept">$affiliation.department$</institution>
+$endif$
+<institution-wrap>
+$if(affiliation.organization)$
+<institution>$affiliation.organization$</institution>
+$else$
+<institution>$affiliation.name$</institution>
+$endif$
+$if(affiliation.isni)$
+<institution-id institution-id-type="ISNI">$affiliation.isni$</institution-id>
+$endif$
+$if(affiliation.ringgold)$
+<institution-id institution-id-type="Ringgold">$affiliation.ringgold$</institution-id>
+$endif$
+$if(affiliation.ror)$
+<institution-id institution-id-type="ROR">$affiliation.ror$</institution-id>
+$endif$
+</institution-wrap>$if(affiliation.street-address)$,
+$for(affiliation.street-address)$
+<addr-line>$affiliation.street-address$</addr-line>$sep$,
+$endfor$
+$else$$if(affiliation.city)$, <city>$affiliation.city$</city>$endif$$endif$$if(affiliation.country)$,
+<country$if(affiliation.country-code)$ country="$affiliation.country-code$"$endif$>$affiliation.country$</country>$endif$
+</aff>
+$endfor$
--- a/data/templates/article.jats_publishing
+++ b/data/templates/article.jats_publishing
@ -101,14 +101,15 @@ $endif$
 $if(author.email)$
 <email>$author.email$</email>
 $endif$
-$if(author.aff-id)$
-<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
-$endif$
+$for(author.affiliation)$
+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
+$endfor$
 $if(author.cor-id)$
 <xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
 $endif$
 </contrib>
 $endfor$
+${ affiliations.jats() }
 </contrib-group>
 $endif$
 $if(article.author-notes)$
--- a/data/templates/default.jats_articleauthoring
+++ b/data/templates/default.jats_articleauthoring
@ -34,14 +34,15 @@ $endif$
 $if(author.email)$
 <email>$author.email$</email>
 $endif$
-$if(author.aff-id)$
-<xref ref-type="aff" rid="aff-$contrib.aff-id$"/>
-$endif$
+$for(author.affiliation)$
+<xref ref-type="aff" rid="aff-$author.affiliation$"/>
+$endfor$
 $if(author.cor-id)$
 <xref ref-type="corresp" rid="cor-$author.cor-id$"><sup>*</sup></xref>
 $endif$
 </contrib>
 $endfor$
+${ affiliations.jats() }
 </contrib-group>
 $endif$
 $if(copyright)$
--- a/doc/jats.md
+++ b/doc/jats.md
@ -39,6 +39,12 @@ Metadata Values
        Used as the contents of the [`<email>`][elem:given-names]
        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
@ -48,6 +54,73 @@ Metadata Values
        [`rid`][attr: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`][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`.
+
+    `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>`][elem:permissions] element.
@ -258,7 +331,10 @@ Required metadata values:
  `journal.pmc`.
 - One or more of `journal.pissn`, `journal.eissn`.

+[Ringgold]: https://ringgold.com/
+[attr:content-type]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/attribute/content-type.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
@ -297,3 +373,11 @@ Required metadata values:
 [elem:subject]: https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/subject.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
+[`<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