org-ref & helm-bibtex notes

org-ref & helm-bibtex notes

[Julian Burgos]

Dear list,

I have been using org-ref for a while, using reftex to insert citations in
my org documents.  Now I am switching to helm-bibtex, which is pretty
awesome.  I have a couple of question about the note files.  Org-ref uses
a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
notes are kept in separate files, one per article.  My questions are:

a) Do you have a preference in the single file vs multiple files question?
 Are advantages/disadvantages?  I tend to prefer the single file option,
it makes search easy and also I can add TODO items that later I can pull
out in the agenda view.  With multiple files this would not be as easy. 
Do you agree?

b) Helm-bibtex identifies which references have a note file, adding a
symbol on the reference list.  Can we make helm-bibtex look into a single
file (say the "notes.org" file), look for the :Custom_ID: properties of
the entries, and use that to mark the reference list?  I am teaching
myself emacs-lisp but this is above my capacity right now.

Many thanks,

Julian

Re: org-ref & helm-bibtex notes

[Tory S. Anderson]

Yeah, helm bibtex is awesome. This has been a major topic of discussion in the module development. See: https://github.com/tmalsburg/helm-bibtex/issues/40

Last I talked with the developer, he was thinking hard about it and had maybe even started development on single-note file options. 

"Julian Burgos" <julian@hafro.is> writes:

> Dear list,
>
> I have been using org-ref for a while, using reftex to insert citations in
> my org documents.  Now I am switching to helm-bibtex, which is pretty
> awesome.  I have a couple of question about the note files.  Org-ref uses
> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
> notes are kept in separate files, one per article.  My questions are:
>
> a) Do you have a preference in the single file vs multiple files question?
>  Are advantages/disadvantages?  I tend to prefer the single file option,
> it makes search easy and also I can add TODO items that later I can pull
> out in the agenda view.  With multiple files this would not be as easy. 
> Do you agree?
>
> b) Helm-bibtex identifies which references have a note file, adding a
> symbol on the reference list.  Can we make helm-bibtex look into a single
> file (say the "notes.org" file), look for the :Custom_ID: properties of
> the entries, and use that to mark the reference list?  I am teaching
> myself emacs-lisp but this is above my capacity right now.
>
> Many thanks,
>
> Julian

Re: org-ref & helm-bibtex notes

[John Kitchin]

Julian Burgos writes:

> Dear list,
>
> I have been using org-ref for a while, using reftex to insert citations in
> my org documents.  Now I am switching to helm-bibtex, which is pretty
> awesome.  I have a couple of question about the note files.  Org-ref uses
> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
> notes are kept in separate files, one per article.  My questions are:
>
> a) Do you have a preference in the single file vs multiple files question?
>  Are advantages/disadvantages?  I tend to prefer the single file option,
> it makes search easy and also I can add TODO items that later I can pull
> out in the agenda view.

I prefer the single file, for the reasons you describe.

> With multiple files this would not be as easy.
> Do you agree?
This is not totally true. You can add your directory of org notes to
your org-agenda-files, e.g.

(setq org-agenda-files '("~/path/to/org-notes"))

and it will add all org files in that directory to your agenda. If you
use helm, it is probably easy to search all of the files too.

--
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: org-ref & helm-bibtex notes

[Titus von der Malsburg]

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On 2015-06-16 Tue 17:39, Julian Burgos wrote:
> Dear list,
>
> I have been using org-ref for a while, using reftex to insert citations in
> my org documents.  Now I am switching to helm-bibtex, which is pretty
> awesome.  I have a couple of question about the note files.  Org-ref uses
> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
> notes are kept in separate files, one per article.  My questions are:
>
> a) Do you have a preference in the single file vs multiple files question?
>  Are advantages/disadvantages?  I tend to prefer the single file option,
> it makes search easy and also I can add TODO items that later I can pull
> out in the agenda view.  With multiple files this would not be as easy. 
> Do you agree?

Hi, I’m the author of helm-bibtex.  There was recently a discussion about
this on Github:

  https://github.com/tmalsburg/helm-bibtex/issues/40

Someone convinced me that storing all notes in one file is better and
there is an experimental (and incomplete) implementation in a topic
branch:

  https://github.com/tmalsburg/helm-bibtex/tree/note-files

(Multiple note files will still be possible for users who prefer that.)

> b) Helm-bibtex identifies which references have a note file, adding a
> symbol on the reference list.  Can we make helm-bibtex look into a single
> file (say the "notes.org" file), look for the :Custom_ID: properties of
> the entries, and use that to mark the reference list?  I am teaching
> myself emacs-lisp but this is above my capacity right now.

Yes, something like that needs to be included.  The unresolved question
is how BibTeX keys should be stored in the notes file.  I find property
drawers incredibly clunky and in my experience they can considerably
slow down Emacs in large org files (that’s the reason why I don’t use
org-contacts as much as a would like).

My current favorite format for entries in the notes file is the
following:

  * Author: Title (year)                       :BibTeXkey:
  Here are the notes …

The only problem I see with this is that BibTeX allows keys to contain
colons, and a key with a colon would break org’s tag syntax.

Suggestions welcome.

  Titus


>
> Many thanks,
>
> Julian


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Re: org-ref & helm-bibtex notes

[Julian Burgos]

Thanks John.  You are right, although I think having to read too many org
files would make the agenda run slower.  And creates a lot of buffers (one
per file) which makes navigation more complicated.  I always wished that
the agenda would close those buffers.  Anyway, I think that having a
single file is the best option.

>
> Julian Burgos writes:
>
>> Dear list,
>>
>> I have been using org-ref for a while, using reftex to insert citations
>> in
>> my org documents.  Now I am switching to helm-bibtex, which is pretty
>> awesome.  I have a couple of question about the note files.  Org-ref
>> uses
>> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes
>> that
>> notes are kept in separate files, one per article.  My questions are:
>>
>> a) Do you have a preference in the single file vs multiple files
>> question?
>>  Are advantages/disadvantages?  I tend to prefer the single file option,
>> it makes search easy and also I can add TODO items that later I can pull
>> out in the agenda view.
>
> I prefer the single file, for the reasons you describe.
>
>> With multiple files this would not be as easy.
>> Do you agree?
> This is not totally true. You can add your directory of org notes to
> your org-agenda-files, e.g.
>
> (setq org-agenda-files '("~/path/to/org-notes"))
>
> and it will add all org files in that directory to your agenda. If you
> use helm, it is probably easy to search all of the files too.
>
> --
> 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: org-ref & helm-bibtex notes

[Julian Burgos]

Hi Titus,

I think a very simple template for the notes file would suffice.  I am
using org ref and had originally modified the template by removing the
TODO, simplifying the properties drawer (no need to duplicate all the
biblatex info here) and adding a link to the pdf file, which is very handy
when reading my notes file.

* [[/path/to/pdf/files/BibTeXkey.pdf][BibTeXkey]] Title
:PROPERTIES:
:Custom_ID: BibTeXkey
:END:

Recently I upgraded org-ref and instead of using my own link to the pdf
file, I use a "cite" statement, which gives me all the goodies from
org-ref (opening the pdf file, accesing Google Scholar, etc.etc.).

* cite:BibTeXkey Title
:PROPERTIES:
:Custom_ID: BibTeXkey
:END:

I have no choice between using drawers or tags.  I have not experienced
slow downs because of using drawers, although tags would make the notes
file look cleaner.  The issue with keys containing colons could be solved
by replacing the colon with some other acceptable character on the tag,
like "@" or "_".  So a reference with BibTeXkey "Smith,Jones 2008" would
get a tag "Smith@Jones2008" or "Smith_Jones2008".

Julian


>
> On 2015-06-16 Tue 17:39, Julian Burgos wrote:
>> Dear list,
>>
>> I have been using org-ref for a while, using reftex to insert citations
>> in
>> my org documents.  Now I am switching to helm-bibtex, which is pretty
>> awesome.  I have a couple of question about the note files.  Org-ref
>> uses
>> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes
>> that
>> notes are kept in separate files, one per article.  My questions are:
>>
>> a) Do you have a preference in the single file vs multiple files
>> question?
>>  Are advantages/disadvantages?  I tend to prefer the single file option,
>> it makes search easy and also I can add TODO items that later I can pull
>> out in the agenda view.  With multiple files this would not be as easy.
>> Do you agree?
>
> Hi, I’m the author of helm-bibtex.  There was recently a discussion about
> this on Github:
>
>   https://github.com/tmalsburg/helm-bibtex/issues/40
>
> Someone convinced me that storing all notes in one file is better and
> there is an experimental (and incomplete) implementation in a topic
> branch:
>
>   https://github.com/tmalsburg/helm-bibtex/tree/note-files
>
> (Multiple note files will still be possible for users who prefer that.)
>
>> b) Helm-bibtex identifies which references have a note file, adding a
>> symbol on the reference list.  Can we make helm-bibtex look into a
>> single
>> file (say the "notes.org" file), look for the :Custom_ID: properties of
>> the entries, and use that to mark the reference list?  I am teaching
>> myself emacs-lisp but this is above my capacity right now.
>
> Yes, something like that needs to be included.  The unresolved question
> is how BibTeX keys should be stored in the notes file.  I find property
> drawers incredibly clunky and in my experience they can considerably
> slow down Emacs in large org files (that’s the reason why I don’t use
> org-contacts as much as a would like).
>
> My current favorite format for entries in the notes file is the
> following:
>
>   * Author: Title (year)                       :BibTeXkey:
>   Here are the notes …
>
> The only problem I see with this is that BibTeX allows keys to contain
> colons, and a key with a colon would break org’s tag syntax.
>
> Suggestions welcome.
>
>   Titus
>
>
>>
>> Many thanks,
>>
>> Julian
>
>

Re: org-ref & helm-bibtex notes

[Titus von der Malsburg]

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On 2015-06-16 Tue 18:28, Titus von der Malsburg wrote:
> On 2015-06-16 Tue 17:39, Julian Burgos wrote:
>> Dear list,
>>
>> I have been using org-ref for a while, using reftex to insert citations in
>> my org documents.  Now I am switching to helm-bibtex, which is pretty
>> awesome.  I have a couple of question about the note files.  Org-ref uses
>> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
>> notes are kept in separate files, one per article.  My questions are:
>>
>> a) Do you have a preference in the single file vs multiple files question?
>>  Are advantages/disadvantages?  I tend to prefer the single file option,
>> it makes search easy and also I can add TODO items that later I can pull
>> out in the agenda view.  With multiple files this would not be as easy. 
>> Do you agree?
>
> Hi, I’m the author of helm-bibtex.  There was recently a discussion about
> this on Github:
>
>   https://github.com/tmalsburg/helm-bibtex/issues/40
>
> Someone convinced me that storing all notes in one file is better and
> there is an experimental (and incomplete) implementation in a topic
> branch:
>
>   https://github.com/tmalsburg/helm-bibtex/tree/note-files

Update: I worked on the note-files branch and as far as I’m concerned it
is ready to be merged into master.  There are several changes:

When one big notes file is used:

- The new default template for notes is simpler than what org-ref uses
  but it should be compatible because it uses the Custom_ID property to
  store the key.
- Note templates can be defined in `helm-bibtex-notes-template`.
- The list of publications now shows a mark if notes are available for a
  publication.
- Finding the correct entry is now robust because the code looks for
  `Custom_ID: key` not just for the key.

Multiple note files (one for each publication):

- The template for notes is used to populate new note
  files.  (Previously it was only used in the case with one big notes
  file.)

Julian, if you could test this branch, that would be fantastic!

Here is the code:

  https://github.com/tmalsburg/helm-bibtex/tree/note-files

Titus

>
> (Multiple note files will still be possible for users who prefer that.)
>
>> b) Helm-bibtex identifies which references have a note file, adding a
>> symbol on the reference list.  Can we make helm-bibtex look into a single
>> file (say the "notes.org" file), look for the :Custom_ID: properties of
>> the entries, and use that to mark the reference list?  I am teaching
>> myself emacs-lisp but this is above my capacity right now.
>
> Yes, something like that needs to be included.  The unresolved question
> is how BibTeX keys should be stored in the notes file.  I find property
> drawers incredibly clunky and in my experience they can considerably
> slow down Emacs in large org files (that’s the reason why I don’t use
> org-contacts as much as a would like).
>
> My current favorite format for entries in the notes file is the
> following:
>
>   * Author: Title (year)                       :BibTeXkey:
>   Here are the notes …
>
> The only problem I see with this is that BibTeX allows keys to contain
> colons, and a key with a colon would break org’s tag syntax.
>
> Suggestions welcome.
>
>   Titus
>
>
>>
>> Many thanks,
>>
>> Julian


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