should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[John Kitchin]

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The org-cite-list-bibliography-files function in oc.el returns a
combination of file-local files and the bibfiles defined
in org-cite-global-bibliography.

It seems like that should not be the case, i.e. if you define BIBLIOGRAPHY
keywords it means you do not want to use the ones
in org-cite-global-bibliography. Is there a scenario where the union of
those makes sense?

John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

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Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Bruce D'Arcus]

I was wondering about this the other day too, and am not sure.

It can actually be a problem, and has been for me, if you're mixing
export processors; like biblatex, and CSL (which is best to use with
json currently).

So I definitely see a downside currently, and can't think of a problem
in changing this.

If someone else can, maybe it should be configurable?

Along these lines, it might be nice if we could choose which global
file(s) or extensions for which processor.

On Mon, Jul 19, 2021 at 12:07 PM John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
> The org-cite-list-bibliography-files function in oc.el returns a combination of file-local files and the bibfiles defined in org-cite-global-bibliography.
>
> It seems like that should not be the case, i.e. if you define BIBLIOGRAPHY keywords it means you do not want to use the ones in org-cite-global-bibliography. Is there a scenario where the union of those makes sense?
>
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Vikas Rawal]

> It seems like that should not be the case, i.e. if you define BIBLIOGRAPHY
> keywords it means you do not want to use the ones
> in org-cite-global-bibliography. Is there a scenario where the union of those
> makes sense?

I second this. The local bibliographies should supercede the global.

Vikas

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Thomas S. Dye]

I used to have a global bibliography that my employees all used. 
Every project also had a local bibliography for citations that 
didn't appear in the global bibliography.  At the end of a 
project, after the editor had cleaned up the local bibliography, 
I'd merge it with the global bibliography using a utility called 
bibtool.

hth,
Tom

Vikas Rawal <vikasrawal@gmail.com> writes:

>> It seems like that should not be the case, i.e. if you define 
>> BIBLIOGRAPHY
>> keywords it means you do not want to use the ones
>> in org-cite-global-bibliography. Is there a scenario where the 
>> union of those
>> makes sense?
>
> I second this. The local bibliographies should supercede the 
> global.
>
> Vikas


--
Thomas S. Dye
https://tsdye.online/tsdye

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Bruce D'Arcus]

As Emmenuel pointed out, we missed that Nicolas already thought of
this, and you can do this:

#+org-cite-global-bibliography: nil

With that, there's no problem, and lots of flexibility.

On Mon, Jul 19, 2021 at 8:53 PM Thomas S. Dye <tsd@tsdye.online> wrote:
>
> I used to have a global bibliography that my employees all used.
> Every project also had a local bibliography for citations that
> didn't appear in the global bibliography.  At the end of a
> project, after the editor had cleaned up the local bibliography,
> I'd merge it with the global bibliography using a utility called
> bibtool.
>
> hth,
> Tom
>
> Vikas Rawal <vikasrawal@gmail.com> writes:
>
> >> It seems like that should not be the case, i.e. if you define
> >> BIBLIOGRAPHY
> >> keywords it means you do not want to use the ones
> >> in org-cite-global-bibliography. Is there a scenario where the
> >> union of those
> >> makes sense?
> >
> > I second this. The local bibliographies should supercede the
> > global.
> >
> > Vikas
>
>
> --
> Thomas S. Dye
> https://tsdye.online/tsdye
>

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Eric S Fraga]

On Monday, 19 Jul 2021 at 14:52, Thomas S. Dye wrote:
> I used to have a global bibliography that my employees all used. Every
> project also had a local bibliography for citations that didn't appear
> in the global bibliography.  At the end of a project, after the editor
> had cleaned up the local bibliography, I'd merge it with the global
> bibliography using a utility called bibtool.

Just to add that I do the same.  However, I would have no problem with
local settings overriding the global setting as I would simply add the
global bibliography to the local setting.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-598-g604bfd
: Latest paper written in org: https://arxiv.org/abs/2106.05096

should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[CHARPENTIER Emmanuel via General discussions about Org-mode.]

> It seems like that should not be the case, i.e. if you define
> BIBLIOGRAPHY keywords it means you do not want to use the ones in 
> org-cite-global-bibliography. Is there a scenario where the union of 
> those makes sense?

Yes indeed: you may have
  - A library for background issues (e. g. methodology)
  - A (or several) subject matter-specific library (e. g. a 
    subdiscipline, a method, etc...)
  - A library specific to the question you are discussing (e. g. 
    results of a bibliographic search specific to your question).

The first one is a perfect target for org-cite-global-bibliography. The
last one is of course a target for #+BIBLIOGRAPHY ; I'd tend to let the
subject matter library as a file-specific #+BIBLIOGRAPHY (my subject
matters tend to vary...), but this depends on your field.

You may also think of this typology as books, reviews and research
papers respectively...

HTH,

--
Emmanuel Charpentier

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Bruce D'Arcus]

Yes, you're right Emmanuel.

I guess this goes back to my file type/extension issue then.

I do expect this to be a non-issue in time though, as related packages
update to fully support all three common input formats.

On Mon, Jul 19, 2021 at 1:29 PM CHARPENTIER Emmanuel
<emmanuel.charpentier@aphp.fr> wrote:
>
> > It seems like that should not be the case, i.e. if you define
> > BIBLIOGRAPHY keywords it means you do not want to use the ones in
> > org-cite-global-bibliography. Is there a scenario where the union of
> > those makes sense?
>
> Yes indeed: you may have
>   - A library for background issues (e. g. methodology)
>   - A (or several) subject matter-specific library (e. g. a
>     subdiscipline, a method, etc...)
>   - A library specific to the question you are discussing (e. g.
>     results of a bibliographic search specific to your question).
>
> The first one is a perfect target for org-cite-global-bibliography. The
> last one is of course a target for #+BIBLIOGRAPHY ; I'd tend to let the
> subject matter library as a file-specific #+BIBLIOGRAPHY (my subject
> matters tend to vary...), but this depends on your field.
>
> You may also think of this typology as books, reviews and research
> papers respectively...
>
> HTH,
>
> --
> Emmanuel Charpentier
>

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[John Kitchin]

That doesn't seem consistent with other ways that file-local keywords
are used though, and it would lead (for me anyway) to citing unintended
references (and including unintended bib files in the export) if there is
only one bibliography file that should be used for a document.

Maybe a reasonable compromise is something like

#+bibliography: :local t

which could indicate not to use the global variable.



Bruce D'Arcus <bdarcus@gmail.com> writes:

> Yes, you're right Emmanuel.
>
> I guess this goes back to my file type/extension issue then.
>
> I do expect this to be a non-issue in time though, as related packages
> update to fully support all three common input formats.
>
> On Mon, Jul 19, 2021 at 1:29 PM CHARPENTIER Emmanuel
> <emmanuel.charpentier@aphp.fr> wrote:
>>
>> > It seems like that should not be the case, i.e. if you define
>> > BIBLIOGRAPHY keywords it means you do not want to use the ones in
>> > org-cite-global-bibliography. Is there a scenario where the union of
>> > those makes sense?
>>
>> Yes indeed: you may have
>>   - A library for background issues (e. g. methodology)
>>   - A (or several) subject matter-specific library (e. g. a
>>     subdiscipline, a method, etc...)
>>   - A library specific to the question you are discussing (e. g.
>>     results of a bibliographic search specific to your question).
>>
>> The first one is a perfect target for org-cite-global-bibliography. The
>> last one is of course a target for #+BIBLIOGRAPHY ; I'd tend to let the
>> subject matter library as a file-specific #+BIBLIOGRAPHY (my subject
>> matters tend to vary...), but this depends on your field.
>>
>> You may also think of this typology as books, reviews and research
>> papers respectively...
>>
>> HTH,
>>
>> --
>> Emmanuel Charpentier
>>


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu
Pronouns: he/him/his

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[Bruce D'Arcus]

On Mon, Jul 19, 2021 at 1:54 PM John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> Maybe a reasonable compromise is something like
>
> #+bibliography: :local t
>
> which could indicate not to use the global variable.

I like it!

Bruce

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

[CHARPENTIER Emmanuel via General discussions about Org-mode.]

Le lundi 19 juillet 2021 à 13:54 -0400, John Kitchin a écrit :
> That doesn't seem consistent with other ways that file-local keywords
> are used though, and it would lead (for me anyway) to citing
> unintended
> references (and including unintended bib files in the export) if
> there is
> only one bibliography file that should be used for a document.

You mean you want to do something like \nocite{*} ?

> 
> Maybe a reasonable compromise is something like
> 
> #+bibliography: :local t
> 
> which could indicate not to use the global variable.

No need :

# Local Variables:
# org-cite-global-bibliography: nil
# End:

> 
> 
> 
> Bruce D'Arcus <bdarcus@gmail.com> writes:
> 
> > Yes, you're right Emmanuel.
> > 
> > I guess this goes back to my file type/extension issue then.
> > 
> > I do expect this to be a non-issue in time though, as related
> > packages
> > update to fully support all three common input formats.
> > 
> > On Mon, Jul 19, 2021 at 1:29 PM CHARPENTIER Emmanuel
> > <emmanuel.charpentier@aphp.fr> wrote:
> > > 
> > > > It seems like that should not be the case, i.e. if you define
> > > > BIBLIOGRAPHY keywords it means you do not want to use the ones
> > > > in
> > > > org-cite-global-bibliography. Is there a scenario where the
> > > > union of
> > > > those makes sense?
> > > 
> > > Yes indeed: you may have
> > >   - A library for background issues (e. g. methodology)
> > >   - A (or several) subject matter-specific library (e. g. a
> > >     subdiscipline, a method, etc...)
> > >   - A library specific to the question you are discussing (e. g.
> > >     results of a bibliographic search specific to your question).
> > > 
> > > The first one is a perfect target for org-cite-global-
> > > bibliography. The
> > > last one is of course a target for #+BIBLIOGRAPHY ; I'd tend to
> > > let the
> > > subject matter library as a file-specific #+BIBLIOGRAPHY (my
> > > subject
> > > matters tend to vary...), but this depends on your field.
> > > 
> > > You may also think of this typology as books, reviews and
> > > research
> > > papers respectively...
> > > 
> > > HTH,
> > > 
> > > --
> > > Emmanuel Charpentier
> > > 
> 
> 
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
> Pronouns: he/him/his