Re: [jats-list] table-wrap-foot example with fn-group

Subject: Re: [jats-list] table-wrap-foot example with fn-group
From: Tommie Usdin <btusdin@xxxxxxxxxxxxxxxx>
Date: Fri, 7 Mar 2014 16:09:44 -0500
Alf 

There are many situations in which JATS allows multiple ways to encode the
same content; footnotes are one of these. JATS *allows* the user to wrap <fn>s
in <fn-group>s but does not require it. There are systems (for example many
typesetting applications) that work far more gracefully if footnotes, tables,
and figures are grouped than if they are interspersed in the text. There are
other systems (many that render content on the web) that work more gracefully
if these floating objects are in the file close to the first place they are
referenced.

This flexibility in the JATS specification is appropriate; one of the goals of
the JATS design is that it should be compatible with the variety of encoding
practices produced by journal publishers before JATS was developed and
compatible with the variety of systems that ingest tagged journal articles.

It is also appropriate that a particular recipient of JATS content has
guidelines that specify which of the options allowed in JATS are acceptable to
that recipient. PubMed Central is one of many (hundreds? thousands?) of
organizations that ingest documents in JATS. PMC's guidelines specify what I
think of as a profile of JATS; the way their systems want to receive the
documents. And their style checker checks documents to see that they are both
legal JATS *AND* compatible with their preferred usage of JATS.

I do not know why PMC prefers the coding options they specify, I suspect it
has to do with the way their ingest systems were developed and the way they
have evolved over time. Other libraries, archives, and services have specified
other coding options, probably because their tools work best with other coding
styles.

The samples in the JATS documentation reflect the variety of users/uses of the
JATS. Sometimes they match PMCs preferences, sometimes they do not. The JATS
documentation is not intended to be PMC documentation. It may be that it would
be good if additional examples were added to the JATS documentation to show
other ways in which JATS documents can be tagged.

This is a long way to say that there is no one common usage of the JATS. (If
you look at the chapters in the JATS Tag Libraries under Common Tagging
Practice you will see that most of these discussion show several ways in
which content can be tagged. See, for example, "Tagging Figures, Graphics, and
Multimedia under Common Tagging Practice in any of the Tag Libraries.) The
samples in the JATS documentation illustrate one/some ways these structures
can be used but are not intended to match any particular user profile.

I hope this is helpful.

 Tommie




On Mar 7, 2014, at 6:51 AM, Alf Eaton <eaton.alf@xxxxxxxxx> wrote:

> Although the example in the JATS documentation for
> <table-wrap-foot>[1] contains multiple <fn> elements wrapped in an
> <fn-group>, PubMed Central's Style Checker complains about this usage
> and wants the <fn> elements to be direct children of the
> <table-wrap-foot>.
>
> As there's presumably some good reasoning behind PMC's choice (not
> documented, other than "Tag table footnotes in <table-wrap-foot>"[2],
> would it be useful to update the example to be in line with common
> usage, unless there's some particular reason for <fn-group> to be used
> in this location?
>
> I've experienced this error/warning in practice, and have edited the
> <fn-group> out of some article XML to comply with the PMC guidelines.
>
> Alf
>
> [1]
http://jats.nlm.nih.gov/publishing/tag-library/1.1d1/?elem=table-wrap-foot
> [2]
http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/tags.html#j
v1d2e7850
>

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