Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ypo]

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I have a .bib file with references, and a .org file with annotations. Like:

.bib file:

> @book{Saul.2013.DoctorYourselfNaturalHealing,
>   title = {Doctor yourself: natural healing that works},
>   shorttitle = {Doctor yourself},
>   author = {Saul, Andrew W},
>   year = {2013},
>   publisher = {Basic Health Publications},
>   address = {Laguna Beach, CA},
>   isbn = {978-1-59120-310-0},
>   language = {English},
>   annotation = {OCLC: 883386139}
> }
>
>
> .org file:
>
> ** Saul, A. W. (2013). /Doctor yourself: Natural healing that works. 
> Basic Health Publications./
>    :PROPERTIES:
>    :ID:       20210821T132443.642438
>    :END:
>  [[file:data/Saul.2012.DoctorYourself.mobi]]
>
> *** Saul, A. W. (2012) "Vitamin D"
> Supplements represent an efficient way to obtain sufficient vitamin D. 
> African-Americans should consider taking 3,000 international units 
> (IU) per day while White Americans should consider taking 2,000 
> IU/day. The current dietary guideline, approximately 400 IU/day, was 
> based on the amount of vitamin D in a spoonful of cod liver oil, which 
> prevented rickets.
>
> There are few adverse effects of vitamin D. With whole-body exposure 
> to the sun, one can make at least 10,000 IU/day in a short time. 
> _Adverse effects such as hypercalcemia have been found in general only 
> for 20,000–40,000 IU/day for very long periods._ However, those with 
> certain diseases such as adenoma of the parathyroid gland, 
> granulomatous diseases, lymphoma, sarcoidosis, and tuberculosis, 
> should limit their vitamin D intake or production due to the fact that 
> the body’s innate immune system produces too much 
> 1,25-dihydroxyvitamin D in the serum, which can raise serum calcium 
> levels too high.
>
> ...
>

Could I write on the .bib file using the orgmode power? Something like 
this could work as a .bib file, or is it a no-no?

>
> ** Saul, A. W. (2013). /Doctor yourself: Natural healing that works. 
> Basic Health Publications./
>    :PROPERTIES:
>    :ID:       20210821T132443.642438
>    :END:
>  [[file:data/Saul.2012.DoctorYourself.mobi]]
>
>
> @book{Saul.2013.DoctorYourselfNaturalHealing,
>   title = {Doctor yourself: natural healing that works},
>   shorttitle = {Doctor yourself},
>   author = {Saul, Andrew W},
>   year = {2013},
>   publisher = {Basic Health Publications},
>   address = {Laguna Beach, CA},
>   isbn = {978-1-59120-310-0},
>   language = {English},
>   annotation = {OCLC: 883386139}
> }
>
>
> *** Saul, A. W. (2012) "Vitamin D"
> Supplements represent an efficient way to obtain sufficient vitamin D. 
> African-Americans should consider taking 3,000 international units 
> (IU) per day while White Americans should consider taking 2,000 
> IU/day. The current dietary guideline, approximately 400 IU/day, was 
> based on the amount of vitamin D in a spoonful of cod liver oil, which 
> prevented rickets.
>
> There are few adverse effects of vitamin D. With whole-body exposure 
> to the sun, one can make at least 10,000 IU/day in a short time. 
> _Adverse effects such as hypercalcemia have been found in general only 
> for 20,000–40,000 IU/day for very long periods._ However, those with 
> certain diseases such as adenoma of the parathyroid gland, 
> granulomatous diseases, lymphoma, sarcoidosis, and tuberculosis, 
> should limit their vitamin D intake or production due to the fact that 
> the body’s innate immune system produces too much 
> 1,25-dihydroxyvitamin D in the serum, which can raise serum calcium 
> levels too high.
>

Best regards,

Ypo


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Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ihor Radchenko]

Ypo <ypuntot@gmail.com> writes:

> I have a .bib file with references, and a .org file with annotations. Like:
> ...
> Could I write on the .bib file using the orgmode power? Something like 
> this could work as a .bib file, or is it a no-no?

M-x org-bibtex (you need a special format for Org headings).  org-bibtex
is a part of ol-bibtex.el.

Also, I wrote a set of helpers to capture bibliographic data into Org
mode headings: https://github.com/yantar92/org-capture-ref

The format is something like:

******* DONE [#A] Nix [Scripta Materialia] (1998) Yielding and strain hardening of thin metal films on substrates :FLAGGED:BOOKMARK:article:ATTACH:
SCHEDULED: <2021-03-08 Mon>
:PROPERTIES:
:TITLE:    Yielding and strain hardening of thin metal films on substrates
:BTYPE:    article
:AUTHOR:   Nix, William D
:JOURNAL:  Scripta Materialia
:VOLUME:   39
:NUMBER:   4-5
:PAGES:    545-554
:YEAR:     1998
:URL:      https://scholar.googleusercontent.com/scholar.bib?q=info:sVHrZR2RlwsJ:scholar.google.com/&output=citation&scisdr=CgXarAaXEL216MPM490:AAGBfm0AAAAAYD3J-917MgTBuwvpZNL09BcZoHmF8au_&scisig=AAGBfm0AAAAAYD3J-ytYquMZbiTcC-Jxg3itxnjKSZfQ&scisf=4&ct=citation&cd=-1&hl=en
:CREATED:  [2021-03-02 Tue 13:25]
:HOWPUBLISHED: Scholar.Googleusercontent
:NOTE:     Online; accessed 02 March 2021
:PUBLISHER: Pergamon
:ID:       2c5b442a-c8fa-43d2-86f0-c160b496eb4d
:Effort:   0:05
:SHOWFROMDATE: 2021-03-08
:END:

 #CLS #dislocation #misfit #theory

- !! [2021-03-09 Tue] [[id:5cc9cea1-a023-4cc8-9753-277dc474850b][Pant Acta 2003]] showed that the hypothesised dislocation/misfit interaction does not actually happen (at least, in (111) FCC films)
  - Yet, the shape of the dislocation upon interaction with the misfit is still a "bump", thus general derivation by Nix is still not too terrible. *The Nix's model just overestimate the hardening*

This headings exports to

@article{2c5b442a-c8fa-43d2-86f0-c160b496eb4d,
  author={Nix, William D},
  title={Yielding and strain hardening of thin metal films on substrates},
  journal={Scripta Materialia},
  year={1998},
  volume={39},
  number={4-5},
  pages={545-554},
  note={Online; accessed 02 March 2021}
}

Hope it helps.

Best,
Ihor

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[András Simonyi]

Dear Ypo,

I also think that the org-bibtex format is pretty close to what you
are looking for. An added benefit could be that the org-cite CSL
export processor has recently gained (admittedly rather experimental)
support for directly using org-bibtex bibliographies, although insert
and follow functionality is missing at the moment.

best wishes,
András

On Tue, 19 Oct 2021 at 15:23, Ihor Radchenko <yantar92@gmail.com> wrote:
>
> Ypo <ypuntot@gmail.com> writes:
>
> > I have a .bib file with references, and a .org file with annotations. Like:
> > ...
> > Could I write on the .bib file using the orgmode power? Something like
> > this could work as a .bib file, or is it a no-no?
>
> M-x org-bibtex (you need a special format for Org headings).  org-bibtex
> is a part of ol-bibtex.el.
>
> Also, I wrote a set of helpers to capture bibliographic data into Org
> mode headings: https://github.com/yantar92/org-capture-ref
>
> The format is something like:
>
> ******* DONE [#A] Nix [Scripta Materialia] (1998) Yielding and strain hardening of thin metal films on substrates :FLAGGED:BOOKMARK:article:ATTACH:
> SCHEDULED: <2021-03-08 Mon>
> :PROPERTIES:
> :TITLE:    Yielding and strain hardening of thin metal films on substrates
> :BTYPE:    article
> :AUTHOR:   Nix, William D
> :JOURNAL:  Scripta Materialia
> :VOLUME:   39
> :NUMBER:   4-5
> :PAGES:    545-554
> :YEAR:     1998
> :URL:      https://scholar.googleusercontent.com/scholar.bib?q=info:sVHrZR2RlwsJ:scholar.google.com/&output=citation&scisdr=CgXarAaXEL216MPM490:AAGBfm0AAAAAYD3J-917MgTBuwvpZNL09BcZoHmF8au_&scisig=AAGBfm0AAAAAYD3J-ytYquMZbiTcC-Jxg3itxnjKSZfQ&scisf=4&ct=citation&cd=-1&hl=en
> :CREATED:  [2021-03-02 Tue 13:25]
> :HOWPUBLISHED: Scholar.Googleusercontent
> :NOTE:     Online; accessed 02 March 2021
> :PUBLISHER: Pergamon
> :ID:       2c5b442a-c8fa-43d2-86f0-c160b496eb4d
> :Effort:   0:05
> :SHOWFROMDATE: 2021-03-08
> :END:
>
>  #CLS #dislocation #misfit #theory
>
> - !! [2021-03-09 Tue] [[id:5cc9cea1-a023-4cc8-9753-277dc474850b][Pant Acta 2003]] showed that the hypothesised dislocation/misfit interaction does not actually happen (at least, in (111) FCC films)
>   - Yet, the shape of the dislocation upon interaction with the misfit is still a "bump", thus general derivation by Nix is still not too terrible. *The Nix's model just overestimate the hardening*
>
> This headings exports to
>
> @article{2c5b442a-c8fa-43d2-86f0-c160b496eb4d,
>   author={Nix, William D},
>   title={Yielding and strain hardening of thin metal films on substrates},
>   journal={Scripta Materialia},
>   year={1998},
>   volume={39},
>   number={4-5},
>   pages={545-554},
>   note={Online; accessed 02 March 2021}
> }
>
> Hope it helps.
>
> Best,
> Ihor
>
>

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ihor Radchenko]

András Simonyi <andras.simonyi@gmail.com> writes:

> ... An added benefit could be that the org-cite CSL
> export processor has recently gained (admittedly rather experimental)
> support for directly using org-bibtex bibliographies, although insert
> and follow functionality is missing at the moment.

By the way, do I understand correctly that oc-csl.el requires
citeproc-el to be installed? It is not clearly stated in the commentary.

Best,
Ihor

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[András Simonyi]

On Tue, 19 Oct 2021 at 16:08, Ihor Radchenko <yantar92@gmail.com> wrote:

> By the way, do I understand correctly that oc-csl.el requires
> citeproc-el to be installed? It is not clearly stated in the commentary.

Yes, oc-csl.el uses citeproc-el for formatting the citations and the
bibliography. I'm not entirely sure what kind of commentary you are
referring to but the oc-csl.el source code commentary currently says
that

>  The processor relies on the external Citeproc Emacs library, which must be available prior to loading this library.

Should we add something to this? If yes, what is missing in your opinion?

best wishes,
András

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ihor Radchenko]

András Simonyi <andras.simonyi@gmail.com> writes:

>>  The processor relies on the external Citeproc Emacs library, which must be available prior to loading this library.
>
> Should we add something to this? If yes, what is missing in your opinion?

I saw this comment, but I was not sure which library it referred to.
First, I looked in built-in Emacs libearies. No luck. Then, I tried
search ELPA, but still no luck. Same for NonGNU ELPA. Then I tried web
search and saw github/citeproc-el. It confused me, because it is not
exactly "Citeproc Emacs library", but rather "A CSL 1.01 Citation
Processor for Emacs.". I had to look at source file names to verify.

A link to the library source code would be helpful.

Also,

>> ;; Bibliography is defined with the "bibliography" keyword.  It supports files
>> ;; with ".bib", ".bibtex", and ".json" extensions.  References are exported using
>> ;; the "print_bibliography" keyword.

If there is support of ".org", it could be mentioned (with caveats, I guess).

Best,
Ihor

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ypo]

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Not much time these days to thank you for your help, specially Ihor, 
András, Eric.

After thinking about it, I think I will maintain 2 files by now: 1.bib 
and 1.org. with my highlights and other notes.

Best regards :-)

Ypo


El 19/10/2021 a las 16:45, Ihor Radchenko escribió:
> András Simonyi<andras.simonyi@gmail.com>  writes:
>
>>>   The processor relies on the external Citeproc Emacs library, which must be available prior to loading this library.
>> Should we add something to this? If yes, what is missing in your opinion?
> I saw this comment, but I was not sure which library it referred to.
> First, I looked in built-in Emacs libearies. No luck. Then, I tried
> search ELPA, but still no luck. Same for NonGNU ELPA. Then I tried web
> search and saw github/citeproc-el. It confused me, because it is not
> exactly "Citeproc Emacs library", but rather "A CSL 1.01 Citation
> Processor for Emacs.". I had to look at source file names to verify.
>
> A link to the library source code would be helpful.
>
> Also,
>
>>> ;; Bibliography is defined with the "bibliography" keyword.  It supports files
>>> ;; with ".bib", ".bibtex", and ".json" extensions.  References are exported using
>>> ;; the "print_bibliography" keyword.
> If there is support of ".org", it could be mentioned (with caveats, I guess).
>
> Best,
> Ihor

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Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Eric S Fraga]

On Tuesday, 19 Oct 2021 at 22:09, Ihor Radchenko wrote:
> By the way, do I understand correctly that oc-csl.el requires
> citeproc-el to be installed? It is not clearly stated in the commentary.

That's my understanding.
-- 
: Eric S Fraga via Emacs 28.0.60, Org release_9.5-149-g781080
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Eric S Fraga]

I've been using org-bibtex for this: each headline is an item in your
bibliography and you export the contents to a bib file.  So, not quite
what you want as it's not working with a bib file per se.

However, you can read BiBTeX entries (using org-bibtex-read), for
instance from a bib file downloaded from a journal, and write them into
your org file in the right format (org-bibtex-write).  This populates
the properties automatically.  The bib file of all entries in your org
file is created by the org-bibtex function.
-- 
: Eric S Fraga via Emacs 28.0.60, Org release_9.5-149-g781080
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ypo]

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I asked some months ago about the possibility of using an ORG file at 
the same time as bibliography and as a notebook.

https://lists.gnu.org/archive/html/emacs-orgmode/2021-10/msg00619.html


It seems someone is making it possible :-D

https://gist.github.com/andras-simonyi/eda0daa0b677838022fd7c438b6eadfa

https://www.reddit.com/r/emacs/comments/wqjare/comment/iku77h0/?utm_source=share&utm_medium=web2x&context=3





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Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Bruce D'Arcus]

Yes, but there are some tricky performance issues with large org files
that change a lot, since currently citar will reload the file(s)
whenever they change, but an org file that mixes notes and bib data
may change a lot even if the bib data doesn't. If you have everything
in one file, that becomes a problem.

https://github.com/emacs-citar/citar/issues/397#issuecomment-1221604952

On Tue, Aug 23, 2022 at 7:42 AM Ypo <ypuntot@gmail.com> wrote:
>
> I asked some months ago about the possibility of using an ORG file at the same time as bibliography and as a notebook.
>
> https://lists.gnu.org/archive/html/emacs-orgmode/2021-10/msg00619.html
>
>
> It seems someone is making it possible :-D
>
> https://gist.github.com/andras-simonyi/eda0daa0b677838022fd7c438b6eadfa
>
> https://www.reddit.com/r/emacs/comments/wqjare/comment/iku77h0/?utm_source=share&utm_medium=web2x&context=3
>
>
>
>
>

Re: Could a .bib file be edited and organized in an "org-mode" way and still work as a .bib file?

[Ihor Radchenko]

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

> Yes, but there are some tricky performance issues with large org files
> that change a lot, since currently citar will reload the file(s)
> whenever they change, but an org file that mixes notes and bib data
> may change a lot even if the bib data doesn't. If you have everything
> in one file, that becomes a problem.
>
> https://github.com/emacs-citar/citar/issues/397#issuecomment-1221604952

I suggest org-element-cache-map with :next-re ":BTYPE:". It is good
enough even for real-time queries. You can even attach data to Org
headline element. The data will be attached to the relevant Org
headlines as long as buffer edits do not alter those headlines.

-- 
Ihor Radchenko,
Org mode contributor,
Learn more about Org mode at https://orgmode.org/.
Support Org development at https://liberapay.com/org-mode,
or support my work at https://liberapay.com/yantar92