Re: more helm-bibtex/org-ref questions

[Ramon Diaz-Uriarte <rdiaz02@gmail.com>]

Dear John,


On Fri, 26-06-2015, at 22:58, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> You could have multiple file fields I suppose, and adapt [1] to give you
> a choice of which one to open.

That is an intriguing suggestion. I'll try to play with it.

>
> Personally, I have one pdf per bibtex entry, named by the key of the
> entry, in a directory called bibtex-pdfs somewhere defined by
> org-ref-pdf-directory. There are ~1300 pdfs in there now. I always
> access them through helm bibtex.
>
> admittedly, I don't have the SI or other stuff around usually. I don't
> use bibtex to keep track of the directories where I write manuscripts
> either.
>

I don't use bibtex to keep track of the dirs where I write manuscripts
either, but SI et al I often do want to store. The SI more and more as time
goes by, given the current policy of many journals of moving the methods
details to SI ---I could merge PDFs into a single one, but that is another
step.


> You could always make links to these other things in the associated
> notes entry. or put org-links in a bibtex field, and then you can open
> them with C-c o (if you setup links to work everywhere). That way,
> opening the pdf is easy, and opening the other things is just opening
> the entry and running the link open command.

That is a great suggestion. However, I just realized that I would not be
able to then open any of the links in an Android device (where I do part of
my reading) or in, say, JabRef (I'd need to have a script run to reformat
them, but then propagating changes both ways starts getting very
cumbersome).



I need to think some more about this. Thanks for your suggestions.


Best,

R.

>
> Ramon Diaz-Uriarte writes:
>
>> Dear All,
>>
>> (I am not sure this is the appropriate place, but this is neither a bug
>> report nor an feature request about helm-bibtex or org-ref, but a question
>> from ignorance and I am learning quite a bit from the other helm-bibtex
>> questions).
>>
>>
>> How do people deal with multiple files that are logically associated to an
>> entry?
>>
>>
>> I've been used to keeping the main file, supplementary materials,
>> associated code, etc, in a directory per entry. This kind of modus operandi
>> is something I adopted (fell into?)  easily with Zotero and Mendeley. But I
>> am not sure that this is the best way to proceed.
>>
>>
>> If I end up with multiple files per directory, helm-bibtex-find-pdf[1]
>> cannot know which one I want to open. I could keep the main file in the
>> general directory, so it is found directly by helm-bibtex-find-pdf and
>> specify other files (of secondary usage) in the "file" field (and maybe
>> open them via ebib when/if needed)?  But this does not seem
>> elegant. Another is to have an entry per file, with unique key, but this
>> does not seem right.
>>
>>
>>
>> Thanks,
>>
>> R.
>>
>>
>> [1] Thanks to Titus' help
>> (https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is
>> given in the "file" field with the directory name is now within my reach.

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02@gmail.com
       ramon.diaz@iib.uam.es

http://ligarto.org/rdiaz