more helm-bibtex/org-ref questions

more helm-bibtex/org-ref questions

[Ramon Diaz-Uriarte]

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

Re: more helm-bibtex/org-ref questions

[John Kitchin]

You could have multiple file fields I suppose, and adapt [1] to give you
a choice of which one to open.

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.

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.

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.

--
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

Re: more helm-bibtex/org-ref questions

[Ramon Diaz-Uriarte]

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