JATS writer: footnote numbering

JATS writer: footnote numbering

[denis.maier-FfwAq0itz3ofv37vnLkPlQ]

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Hey,
I've just realized that footnotes are not numbered in JATS output. Is that on purpose?
Best,
Denis

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Re: JATS writer: footnote numbering

[John MacFarlane]

<denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org> writes:

> Hey,
> I've just realized that footnotes are not numbered in JATS output. Is that on purpose?
> Best,
> Denis

I'm not sure.  Maybe Albert Krewinkel would know.

Re: JATS writer: footnote numbering

[Albert Krewinkel]

John MacFarlane <jgm-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> writes:

> <denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org> writes:
>
>> Hey,
>> I've just realized that footnotes are not numbered in JATS output. Is that on purpose?
>> Best,
>> Denis
>
> I'm not sure.  Maybe Albert Krewinkel would know.

I think we just went with the examples in the documentation, which
happens not to specify any numbers. Regardless, we should probably add a
<label> with the number to the <fn>. Would you open an issue for this?

To hijack this thread with another question: any suggestions what tags
to use for spans? I found yesterday that pandoc is still using
<milestone-start> and <milestone-end>, which were in JATS version 1.1
but are not in 1.2. The <target> element could be fitting, or maybe
<named-content> or <styled-content>?

--
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

AW: JATS writer: footnote numbering

[denis.maier-FfwAq0itz3ofv37vnLkPlQ]

> -----Ursprüngliche Nachricht-----
> Von: Albert Krewinkel <albert+pandoc-9EawChwDxG8hFhg+JK9F0w@public.gmane.org>
> Gesendet: Dienstag, 6. April 2021 18:20
> An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> Cc: Maier, Denis Christian (UB) <denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>;
> attila.torcsvari-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org; Stutzmann, Jan (UB)
> <jan.stutzmann-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>
> Betreff: Re: JATS writer: footnote numbering
> 
> 
> John MacFarlane <jgm-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> writes:
> 
> > <denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org> writes:
> >
> >> Hey,
> >> I've just realized that footnotes are not numbered in JATS output. Is that
> on purpose?
> >> Best,
> >> Denis
> >
> > I'm not sure.  Maybe Albert Krewinkel would know.
> 
> I think we just went with the examples in the documentation, which
> happens not to specify any numbers. Regardless, we should probably add a
> <label> with the number to the <fn>. Would you open an issue for this?

Yes, I'll open an issue. Besides, I've just went through the documentation, and it says:

> In print, footnotes are traditionally displayed at the bottom of a printed page or in a list at the end of the article (<fn-group>); each footnote reference is marked by a number or symbol, and the text of the footnote is prefixed by the same number or symbol to help the reader associate the text with its reference(s). On screen, footnotes may appear as clickable icons, in a separate pop-up window, in a list with links at the end of an article (<fn-group>), or in a separate footnote area.
https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
So, I guess we need to have some flexibility here. Users will perhaps need numbers, symbols or even empty labels depending on purpose and output format.

> 
> To hijack this thread with another question: any suggestions what tags to use
> for spans? I found yesterday that pandoc is still using <milestone-start> and
> <milestone-end>, which were in JATS version 1.1 but are not in 1.2. The
> <target> element could be fitting, or maybe <named-content> or <styled-
> content>?

Yes, <milestone-start/>...<milestone-stop/> is a bit odd although still valid, at least in the archiving tag set. I'm not sure why <target> should be used here. Can you elaborate? Regarding the other two suggestions:
My suggestion would be to go for <named-content>. If I understand correctly, the difference between <named-content> and <styled-content> is rather subtle, but <named-content> deals more with semantics while <styled-content> is more concerned with presentational details.

Denis

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Re: AW: JATS writer: footnote numbering

[Albert Krewinkel]

Another question on the topic of labels: The `<aff>` elements emitted by
pandoc currently don't use labels, mainly because the respective code is
shared between all tag set templates. Labels are not allowed in aff
according to the articleauthoring tag set, so they are omitted for all
flavors. We could stop this sharing and include affiliation labels in
publishing and archiving output. Would that be helpful?

-- 
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

AW: AW: JATS writer: footnote numbering

[denis.maier-FfwAq0itz3ofv37vnLkPlQ]

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FWIW, numbered footnotes have been added to the JATS writer by Albert. Thanks!

Denis

Von: Attila Törcsvári <attila.torcsvari-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
Gesendet: Samstag, 10. April 2021 20:56
An: Albert Krewinkel <albert+pandoc-9EawChwDxG8hFhg+JK9F0w@public.gmane.org>
Cc: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org; Maier, Denis Christian (UB) <denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>; Stutzmann, Jan (UB) <jan.stutzmann-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>
Betreff: Re: AW: JATS writer: footnote numbering

This all can be solved with a filter, placing the footnote number "back" to the beginning of the footnote text, based on the footnote marker found in the main text.
Couple of lines code, e.g., in XSLT.
Attila

On Sat, Apr 10, 2021 at 4:19 PM Albert Krewinkel <albert+pandoc@zeitkraut.de<mailto:albert%2Bpandoc-9EawChwDxG8hFhg+JK9F0w@public.gmane.org>> wrote:
Another question on the topic of labels: The `<aff>` elements emitted by
pandoc currently don't use labels, mainly because the respective code is
shared between all tag set templates. Labels are not allowed in aff
according to the articleauthoring tag set, so they are omitted for all
flavors. We could stop this sharing and include affiliation labels in
publishing and archiving output. Would that be helpful?

--
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

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AW: JATS writer: footnote numbering

[denis.maier-FfwAq0itz3ofv37vnLkPlQ]

Not sure about this. I've had a quick look at the examples given in the tag library, but they all don't use labels in `<aff>` elements. What exactly do you have in mind?

Denis

> -----Ursprüngliche Nachricht-----
> Von: Albert Krewinkel <albert-9EawChwDxG8hFhg+JK9F0w@public.gmane.org>
> Gesendet: Samstag, 10. April 2021 16:17
> An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> Cc: Maier, Denis Christian (UB) <denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>;
> attila.torcsvari-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org; Stutzmann, Jan (UB)
> <jan.stutzmann-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>
> Betreff: Re: JATS writer: footnote numbering
> 
> Another question on the topic of labels: The `<aff>` elements emitted by
> pandoc currently don't use labels, mainly because the respective code is
> shared between all tag set templates. Labels are not allowed in aff according
> to the articleauthoring tag set, so they are omitted for all flavors. We could
> stop this sharing and include affiliation labels in publishing and archiving
> output. Would that be helpful?
> 
> --
> Albert Krewinkel
> GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

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Re: AW: JATS writer: footnote numbering

[Albert Krewinkel]

denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org writes:

> Not sure about this. I've had a quick look at the examples given in
> the tag library, but they all don't use labels in `<aff>` elements.
> What exactly do you have in mind?

I'd do something similar as for footnotes. The markup for articles in
the journal below looks quite reasonable to me (snippet attached), and
we could try to produce something similar. But maybe that would make
pandoc's output too opinionated?

https://doi.org/10.5964/ejop.2567

    <contrib-group>
      <contrib contrib-type="author" corresp="yes">
        <name name-style="western">
          <surname>Çapan</surname>
          <given-names>Dicle</given-names>
        </name>
        <xref ref-type="corresp" rid="cor1">*</xref>
        <xref ref-type="aff" rid="aff1">
          <sup>a</sup>
        </xref>
      </contrib>
      <contrib contrib-type="author">
        <name name-style="western">
          <surname>Ikier</surname>
          <given-names>Simay</given-names>
        </name>
        <xref ref-type="aff" rid="aff2">
          <sup>b</sup>
        </xref>
      </contrib>
      <contrib contrib-type="editor">
        <name>
          <surname>Worth</surname>
          <given-names>Rhian</given-names>
        </name>
        <xref ref-type="aff" rid="aff3" />
      </contrib>
      <aff id="aff1">
      <label>a</label>Department of Psychology, Koç University,
      Istanbul,
      <country>Turkey</country></aff>
      <aff id="aff2">
      <label>b</label>Department of Psychology, Bahçeşehir University,
      Istanbul,
      <country>Turkey</country></aff>
      <aff id="aff3">University of South Wales, Pontypridd,
      <country>United Kingdom</country></aff>
    </contrib-group>

--
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

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AW: AW: JATS writer: footnote numbering

[denis.maier-FfwAq0itz3ofv37vnLkPlQ]

> -----Ursprüngliche Nachricht-----
> Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-
> discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von Albert Krewinkel
> Gesendet: Dienstag, 13. April 2021 08:16
> An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> Cc: attila.torcsvari-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org; Stutzmann, Jan (UB)
> <jan.stutzmann-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org>
> Betreff: Re: AW: JATS writer: footnote numbering
> 
> 
> denis.maier-FfwAq0itz3ofv37vnLkPlQ@public.gmane.org writes:
> 
> > Not sure about this. I've had a quick look at the examples given in
> > the tag library, but they all don't use labels in `<aff>` elements.
> > What exactly do you have in mind?
> 
> I'd do something similar as for footnotes. The markup for articles in the
> journal below looks quite reasonable to me (snippet attached), and we could
> try to produce something similar. But maybe that would make pandoc's
> output too opinionated?

I currently don't need these kind of labels in my journal. But I wouldn't mind either as I can just omit them when going from xml to html and pdf.  So, I'm rather agnostic. 
OTOH, that's indeed something where people's needs may be rather different. Some will want a, b, c, others 1, 2, 3 or x, xx, xxx). So perhaps, it might be reasonable to expect folks to use a filter or post-process with xslt, python or whatever for that. Or just add them manually to the metadata block as we're not talking about 40 affiliations per article, right?

Denis

> 
> https://doi.org/10.5964/ejop.2567
> 
>     <contrib-group>
>       <contrib contrib-type="author" corresp="yes">
>         <name name-style="western">
>           <surname>Çapan</surname>
>           <given-names>Dicle</given-names>
>         </name>
>         <xref ref-type="corresp" rid="cor1">*</xref>
>         <xref ref-type="aff" rid="aff1">
>           <sup>a</sup>
>         </xref>
>       </contrib>
>       <contrib contrib-type="author">
>         <name name-style="western">
>           <surname>Ikier</surname>
>           <given-names>Simay</given-names>
>         </name>
>         <xref ref-type="aff" rid="aff2">
>           <sup>b</sup>
>         </xref>
>       </contrib>
>       <contrib contrib-type="editor">
>         <name>
>           <surname>Worth</surname>
>           <given-names>Rhian</given-names>
>         </name>
>         <xref ref-type="aff" rid="aff3" />
>       </contrib>
>       <aff id="aff1">
>       <label>a</label>Department of Psychology, Koç University,
>       Istanbul,
>       <country>Turkey</country></aff>
>       <aff id="aff2">
>       <label>b</label>Department of Psychology, Bahçeşehir University,
>       Istanbul,
>       <country>Turkey</country></aff>
>       <aff id="aff3">University of South Wales, Pontypridd,
>       <country>United Kingdom</country></aff>
>     </contrib-group>
> 
> --
> Albert Krewinkel
> GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124
> 
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> discuss/874kgad813.fsf%40zeitkraut.de.

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