Re: [jats-list] Linking <contrib> to <aff>

["Alexander Schwarzman aschwarzman@xxxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>]

Hi Ken,

> Have you ever chosen not to include clickable text in these affiliation
cross references, and if so, what would you be expecting during publishing?

Thanks for your question!

My thinking on this has evolved through the years; a good analogy
would be <element-citation> vs. <mixed-citation>.
In the olden days (SGML and early XML), I thought that markup should
be parsimonious, structured, purely semantic, and have as little mixed
content as possible, with the processing systems supplying all
generated text. Several factors have led me to change my mind.

1. Heterogeneity of processing systems
When working with multiple vendors, each using a different PDF
composition engine, there is a risk that the generated text, such as
authors' numeric designators and contribution indicators, will not be
consistent across a publisher's journal portfolio. Another
consideration is that when there is a need to update an article's  PDF
representation, the original composition engine may not be available.
To a lesser extent, the same is true for the XSLTs used to generate an
HTML representation. Including the designators and indicators in the
markup explicitly avoids these issues.

2. Archiving and preservation
Because the reader sees an article in a tangible form, if its XML
source does not contain certain designators and indicators explicitly,
an archive should preserve not only the XML but also the stylesheets.
That is impractical, especially if a publisher does not own the
stylesheets used for PDF composition, nor is this appreciated by the
third-party archives.

3. Search, retrieval, and version consistency
Once the article is rendered, a user may want to use the designators
and indicators for search and retrieval in the source XML. Absence of
those in the source may make tracing cumbersome.

4. QC
Because QC in copyediting may rely on the original manuscript, and QC
in production may rely on the article manifestations, it is more
practical to have the designators and indicators in the XML
explicitly.

These are just a few reasons why, at least for the past couple of
decades, I've been avoiding generated text.

--Sasha

On Tue, Dec 16, 2025 at 5:05b/PM G. Ken Holman g.ken.holman@xxxxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>
> Thank you, Alexander. I see here that you conveniently have supplied
clickable text in your xref elements, and as a publishing service, that
satisfies what my stylesheets' needs.
>
> Have you ever chosen not to include clickable text in these affiliation
cross references, and if so, what would you be expecting during publishing?
>
> At 16/12/2025 17:27 +0000, Alexander Schwarzman aschwarzman@xxxxxxxxx
wrote:
> >Hi Michael,
> >
> >Pieter and Nikos have already weighed in on the problems with not
> >using <xref>, e.g., the need to repeat <aff> when multiple authors
> >share an affiliation, and to indicate @ref-type. I'd like to simply
> >illustrate these points by providing a real-life example from a 2024
> >open-access article; see https://doi.org/10.1364/OE.519379. Here is
> >the relevant portion of the markup:
> >
> ><article-meta>
> >     <contrib-group>
> >          <contrib contrib-type="author">
> >               <name>
> >                    <surname>Collard</surname>
> >                    <given-names>Liam</given-names>
> >               </name>
> >               <xref ref-type="aff" rid="aff1">1</xref>
> >               <xref ref-type="aff" rid="aff2">2</xref>
> >               <xref ref-type="aff" rid="aff4">4</xref>
> >               <xref ref-type="author-notes" rid="an1">\x86</xref>
> >               <xref ref-type="corresp"/>
> >          </contrib>
> >          <contrib contrib-type="author">
> >               <name>
> >                    <surname>Kazemzadeh</surname>
> >                    <given-names>Mohammadrahim</given-names>
> >               </name>
> >               <xref ref-type="aff" rid="aff1">1</xref>
> >               <xref ref-type="aff" rid="aff5">5</xref>
> >               <xref ref-type="author-notes" rid="an1">\x86</xref>
> >          </contrib>
> >          <contrib contrib-type="author">
> >               <name>
> >                    <surname>Piscopo</surname>
> >                    <given-names>Linda</given-names>
> >               </name>
> >               <xref ref-type="aff" rid="aff1">1</xref>
> >               <xref ref-type="aff" rid="aff3">3</xref>
> >          </contrib>
> >          <contrib contrib-type="author">
> >               <name>
> >                    <surname>De Vittorio</surname>
> >                    <given-names>Massimo</given-names>
> >               </name>
> >               <xref ref-type="aff" rid="aff1">1</xref>
> >               <xref ref-type="aff" rid="aff2">2</xref>
> >               <xref ref-type="aff" rid="aff3">3</xref>
> >               <xref ref-type="aff" rid="aff6">6</xref>
> >               <xref ref-type="author-notes" rid="an2">\x87</xref>
> >          </contrib>
> >          <contrib contrib-type="author">
> >               <name>
> >                    <surname>Pisanello</surname>
> >                    <given-names>Ferruccio</given-names>
> >               </name>
> >               <xref ref-type="aff" rid="aff1">1</xref>
> >               <xref ref-type="aff" rid="aff2">2</xref>
> >               <xref ref-type="aff" rid="aff7">7</xref>
> >               <xref ref-type="author-notes" rid="an2">\x87</xref>
> >          </contrib>
> >          <aff
id="aff1"><label>1</label><institution-wrap><institution>Istituto
> >Italiano di
> >               Tecnologia</institution><institution-id
institution-id-type="ror"
> >
>https://ror.org/042t93s57</institution-id></institution-wrap>,
> >Center for Biomolecular Nanotechnologies,
> >               Arnesano, LE 73010, <country
country="IT">Italy</country></aff>
> >          <aff id="aff2"><label>2</label><institution>RAISE
> >Ecosystem</institution>, Genova, <country country="IT"
> >               >Italy</country></aff>
> >          <aff id="aff3"><label>3</label>Dipartimento di Ingegneria
> >DellC"b,b"Innovazione, <institution>Universit\xC3  del
> >               Salento</institution>, Lecce 73100, <country
> >country="IT">Italy</country></aff>
> >          <aff id="aff4">
> >               <label>4</label>
> >               <email>*@iit.it</email>
> >          </aff>
> >          <aff id="aff5">
> >               <label>5</label>
> >               <email>**@iit.it</email>
> >          </aff>
> >          <aff id="aff6">
> >               <label>6</label>
> >               <email>***@iit.it</email>
> >          </aff>
> >          <aff id="aff7">
> >               <label>7</label>
> >               <email>****@iit.it</email>
> >          </aff>
> >     </contrib-group>
> >     <author-notes>
> >          <fn id="an1">
> >               <label>\x86</label>
> >               <p>These authors contributed equally and are co-first
authors</p>
> >          </fn>
> >          <fn id="an2">
> >               <label>\x87</label>
> >               <p>These authors jointly supervised and are co-last
> >authors of this work</p>
> >          </fn>
> >     </author-notes>
> ></article-meta>
> >
> >Thank you,
> >--Sasha
> >
> >Alexander ('Sasha') Schwarzman
> >Content Technology Architect
> >aschwarzman@xxxxxxxxxx
> >Optica Publishing Group
> >
> >
> >
> >
> >On Mon, Dec 15, 2025 at 4:41C"b,B/PM Michael Boudreau
> >mboudreau@xxxxxxxxxxxx <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
> >wrote:
> >>
> >> Hi all,
> >>
> >> I've been discussing with our platform vendor a feature that doesn't
support our practice of linking article authors and their affiliations via
contrib/@rid and aff/@id, e.g.,
> >>
> >> <contrib-group>
> >>     <contrib contrib-type="author" rid="af1">
> >>         <string-name name-style="western">
> >>             <given-names>Sam</given-names>
> >>             <surname>Masur</surname>
> >>         </string-name>
> >>     </contrib>
> >>     <contrib contrib-type="author" rid="af2">
> >>         <string-name name-style="western">
> >>             <given-names>Sadie</given-names>
> >>             <surname>Green</surname>
> >>         </string-name>
> >>     </contrib>
> >>     <aff id="af1">Harvard University</aff>
> >>     <aff id="af2">Massachusetts Institute of Technology</aff>
> >> </contrib-group>
> >>
> >> The vendor points out that the preferred way of linking <contrib> and
<aff> is with a contrib/xref[@ref-type="aff"], which the JATS documentation
indeed labels a "best practice":
https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/contrib.html
> >>
> >> I'm wondering if someone can elaborate on the rationale for recommending
<xref> and whether there's anything inherently problematic with the markup
illustrated above. It strikes me as, at least, simple and unambiguous, well
suited for articles whose authors have a single affiliation, as is extremely
common in the humanities and social sciences.
> >>
> >> --
> >>
> >> Michael R. Boudreau
> >>
> >> Electronic Publishing Technology Manager
> >>
> >> The University of Chicago Press
> >>
> >> 1427 E. 60th Street
> >>
> >> Chicago, IL 60637
> >>
> >> www.journals.uchicago.edu
> >>
> >>
> >>
> >> JATS-List info and archive
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> >
>
>
> --
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