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

["G. Ken Holman g.ken.holman@xxxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>]

Thank you for this, Nikos! I appreciate that you took from your time to share
your observations.

When you say:

>it is expected that the rendering system will potentially come up with the
proper superscripts and labels and render them as you would expect them
without bothering to include all that visual information in the original XML.

Where do I find the documentation for "proper"? In the example, the asterisk
and the sword already are being used for author notes. Those were the first
two obvious symbols to me, and they already are in use.

I understand the need in pumpkin to defer certain things like section labels
to the rendering system. But it had been my understanding until your post
today that from https://jats.nlm.nih.gov/publishing/rationale.html blue was
print ready because it is intended to regularize data. Obviously, I am wrong.

Are there any guidelines to the community on how publishers are to regularize
further the empty cross references that point to items without titles and
labels?

Thank you, again, Nikos.

. . . . . Ken

At 16/12/2025 13:00 +0200, Nikos Markantonatos wrote:
>Hi Ken,
>
>The reason that the sample you reference includes <xref> elements\xC2 with no
actual content and <aff> elements with no labels is because this is a sample
from the JATS Publishing DTD (blue). In this DTD, it is expected that the
rendering system will potentially come up with the proper superscripts and
labels and render them as you would expect them without bothering\xC2 to
include all that visual information in the original XML.
>
>If you are like me and would rather have all that information explicit in the
XML for reasons of archivability and\xC2 preservability, then you should be
looking at the JATS Archiving DTD (green). If you take a look at the
corresponding XML samples for <contrib> in that DTD, you will find all the
superscripts and labels you are looking for:\xC2
<https://jats.nlm.nih.gov/archiving/tag-library/1.4/element/contrib.html>http
s://jats.nlm.nih.gov/archiving/tag-library/1.4/element/contrib.html
>
>Best,
>Nikos
>
>
>On Tue, Dec 16, 2025 at 4:07b/AM G. Ken Holman
<mailto:g.ken.holman@xxxxxxxxx>g.ken.holman@xxxxxxxxx
<<mailto:jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>jats-list-service@xxxxxxxxx
berrytech.com> wrote:
>(trying again but with a properly positioned graphic; apologies for the
bandwidth)
>
>This very topic came up for me at
<https://RealtaOnline.com>https://RealtaOnline.com last week, Michael. Thank
you for bringing this up for discussion.
>
>Personally, I agree with you and I prefer your way and not the recommended
way found in the example at:
>
><https://jats.nlm.nih.gov/publishing/tag-library/1.3/FullArticleSamples/pnas
_sample.xml>https://jats.nlm.nih.gov/publishing/tag-library/1.3/FullArticleSa
mples/pnas_sample.xml
>
><contrib-group>
><contrib contrib-type="author">
><name>
><surname>Sullivan</surname>
><given-names>Amy D.</given-names>
></name>
><xref ref-type="author-notes" rid="FN150">&#x002A;</xref>
><xref ref-type="aff" rid="aff-1"/>
></contrib>
><contrib contrib-type="author">
><name>
><surname>Wigginton</surname>
><given-names>Janis</given-names>
></name>
><xref ref-type="aff" rid="aff-1"/>
></contrib>
><contrib contrib-type="author">
><name>
><surname>Kirschner</surname>
><given-names>Denise</given-names>
></name>
><xref ref-type="author-notes" rid="FN151">&#x2020;</xref>
><xref ref-type="aff" rid="aff-1"/>
></contrib>
></contrib-group>
><aff id="aff-1">Department of Microbiology and Immunology, University
>of Michigan Medical School, Ann Arbor, MI 48109-0620</aff>
>
>Note how the three <xref> elements of ref-type="aff" are empty of content,
and the target <aff> element has no title or label to use as clickable text
for the cross reference. Currently, my XSLT/XSL-FO stylesheet generic fallback
for such a cross reference is to assume this was an authoring error and I use
the identifier as clickable text ... but when this example document came
along, I was disappointed with this visual result:
>
>image.png
>
>
>This begs the question for me "is the recommended empty cross reference only
a semantic link for search or association purposes without any kind of visual
rendering?"
>
>Therefore, should I, as a vendor, assume that a cross reference that has no
clickable content and points to an item that has no identifiable title or
label simply not be rendered because it is assumed to be an internally
expressed semantic or association?
>
>The problem with that assumption, though, is that the documentation doesn't
state what an associated referenced identifier semantic actually is. The
supplied example XML clarifies the semantic by saying ref-type="aff", though I
feel this could be implied by the semantic of the element pointed to by the
referenced identifier.
>
>In your example, I would make the rendered name the clickable text to
visualize the referenced identifier of the affiliation. Would that be an
acceptable rendering to you?
>
>If not, what would you have a vendor do with your specific markup in your
example (if you and I choose not to follow the recommendation)?
>
>Thank you for your insights here.
>
>. . . . . . . Ken
>
>At 15/12/2025 21:41 +0000, Michael Boudreau
<mailto:mboudreau@xxxxxxxxxxxx>mboudreau@xxxxxxxxxxxx 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>
>\xC2  \xC2  <contrib contrib-type="author" rid="af1">
>\xC2  \xC2  \xC2  \xC2  <string-name name-style="western">
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <given-names>Sam</given-names>
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <surname>Masur</surname>
>\xC2  \xC2  \xC2  \xC2  </string-name>
>\xC2  \xC2  </contrib>
>\xC2  \xC2  <contrib contrib-type="author" rid="af2">
>\xC2  \xC2  \xC2  \xC2  <string-name name-style="western">
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <given-names>Sadie</given-names>
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <surname>Green</surname>
>\xC2  \xC2  \xC2  \xC2  </string-name>
>\xC2  \xC2  </contrib>
>\xC2  \xC2  <aff id="af1">Harvard University</aff>
>\xC2  \xC2  <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>http
s://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
><http://www.journals.uchicago.edu>www.journals.uchicago.edu
>\xC2
>JATS-List info and archive
>EasyUnsubscribe (by email)
>
>
>On Mon, Dec 15, 2025 at 4:41b/PM Michael Boudreau
<mailto:mboudreau@xxxxxxxxxxxx>mboudreau@xxxxxxxxxxxx
<<mailto:jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>jats-list-service@xxxxxxxxx
berrytech.com> 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>
>\xC2  \xC2  <contrib contrib-type="author" rid="af1">
>\xC2  \xC2  \xC2  \xC2  <string-name name-style="western">
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <given-names>Sam</given-names>
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <surname>Masur</surname>
>\xC2  \xC2  \xC2  \xC2  </string-name>
>\xC2  \xC2  </contrib>
>\xC2  \xC2  <contrib contrib-type="author" rid="af2">
>\xC2  \xC2  \xC2  \xC2  <string-name name-style="western">
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <given-names>Sadie</given-names>
>\xC2  \xC2  \xC2  \xC2  \xC2  \xC2  <surname>Green</surname>
>\xC2  \xC2  \xC2  \xC2  </string-name>
>\xC2  \xC2  </contrib>
>\xC2  \xC2  <aff id="af1">Harvard University</aff>
>\xC2  \xC2  <aff id="af2">Massachusetts Institute of Technology</aff>
></contrib-group>\xC2
>
>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>http
s://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.
>
>--\xC2
>
>Michael R. Boudreau
>
>Electronic Publishing Technology Manager
>
>The University of Chicago Press
>
>1427 E. 60th\xC2 Street
>
>Chicago, IL 60637
>
><http://www.journals.uchicago.edu>www.journals.uchicago.edu
>
>\xC2
><http://www.mulberrytech.com/JATS/JATS-List/>JATS-List info and archive
><http://lists.mulberrytech.com/unsub/jats-list/2547403>EasyUnsubscribe (by
email)
>
>
>
>--
>Contact info, blog, articles, etc.
<http://www.CraneSoftwrights.com/g/>http://www.CraneSoftwrights.com/g/ |
>Check our site for free XML, XSLT, XSL-FO and UBL developer resources |
>Streaming hands-on XSLT/XPath 2 training class @ US$125(5 hours free) |
>Essays (UBL, XML, etc.)
<http://www.linkedin.com/today/author/gkholman>http://www.linkedin.com/today/
author/gkholman |
><http://www.mulberrytech.com/JATS/JATS-List/>JATS-List info and archive
><http://lists.mulberrytech.com/unsub/jats-list/244090>EasyUnsubscribe (<>by
email)
>
>
>
>--
>Nikos Markantonatos\xC2 | Atypon, Greece Operations Head
>Leoforos Ethnikis Antistaseos 39A, 3rd floor, Nea Ionia, 14234, Greece
>office +30 2110133003\xC2 | mobile +30 6974302945\xC2 |\xC2
<mailto:nikos@xxxxxxxxxx>nikos@xxxxxxxxxx
>\xC2  \xC2  \xC2  \xC2  \xC2 \xC2 \xC2 <http://atypon.com>atypon.com
>CONFIDENTIAL: This email and any attachments may contain confidential and
legally privileged information for the exclusive use of the designated
recipients. Unauthorized review, use, storage, disclosure or distribution is
prohibited. If you are not the intended recipient, contact the sender and
destroy all copies of the original message.
>Content-Type: image/png; name="image.png"
>Content-Disposition: inline; filename="image.png"
>Content-ID: <ii_mj7xwsqn0>
>X-Attachment-Id: ii_mj7xwsqn0
>
>


--
Contact info, blog, articles, etc. http://www.CraneSoftwrights.com/j/ |
Check our site for free XML, XSLT, XSL-FO and UBL developer resources |
Streaming hands-on XSLT/XPath 2 training class @US$50 (5 hours free!) |
Essays (UBL, XML, etc.) http://www.linkedin.com/today/author/gkholman |