Academic Reference Workflows and recommendation of Bibdesk

Academic Reference Workflows and recommendation of Bibdesk

[Chao LU]

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Dear All,

Here I'd like to discuss my workflow for Academic reference and recommend
you Bibdesk.

I use iTune to manage all my mp3 files. Mp3 format has the ability to store
all the metadata into the file itself, and iTune offers a way to modify and
display certain kind of music according to the metadata. Inspired by this, I
was looking for similar way to organize all the academic references and even
to build a personal digital library. I've tried a lot of softwares,
Mendeley, Zotero, Papers, Endnote, Org-mode, Yep, BibDesk...

My feeling is that, Org could get this done, but BibDesk does a better job.
*
1. The Org-mode Way.*
Learned from this mailing list, I think one of the ways to organize academic
references is like below:

Directory structure:
+LibraryRoot
`--- Library.org
`--- Culture/
`--- Mathematics/
`--- Unix/
      `-----Emacs/
`--- .... others

To check in an entry such as "org-manual-7.5.pdf" to the library, one could
do:

Library.org
---------------------------------------------
#+LINK: pdf file:./Emacs/%s.pdf
#+LINK: txt file:./Emacs/%s.txt

* Emacs
** Org-mode
***  Manual of version 7.5
:Emacs:Org:Manual:
:PROPRIETIES:
:Title:
:Author:
:Subject:
:Keywords:
:Comments:
:END:
Location: [[pdf:org-manual-7.5]]
--------------------------------------------
Then use org-attach to get the file settle down in the right place.

To search all the Emacs entries, one could add Library.org to org-agenda
files, then define a related org-agenda command. (It's kind like the smart
group concept in iTune)

However this process is quite time consuming, and non-intuitive. I prefer
the features provided in iTune, Papers2, Bibtex, which could provide
thumbnail and quicklooks of the files.

*2. the Bibdesk way:*
Now I'd like to recommend BibDesk here.

First of all it's free, open resource. Its database file is just an bibtex
file, so all the records is in plain text, even the thumbnails are stored
inside this bibtex file. like below,
=======================
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gk....(It's very
long png source code, so I abridged here)}
=======================

Second, Bibdesk has a much more intuitive UI, and thumbnails are provided.
It also support keywords, smart groups...

Moreover, Bibdesk has a great feature called autofile, which could attach
the file to certain directories (and build the directories structures you
want as well!) Here is the example:

Again, I want to put our org-manual-7.5.pdf into LibraryRoot/Unix/Emacs/

I just have this Bibtex entry ready:

@article{OrgManual:7.5,
    Author = {Org-Mode},
    Date-Added = {2011-06-03 16:07:44 -0400},
    Date-Modified = {2011-06-03 16:14:54 -0400},
    Keywords = {/Unix/Emacs,  Emacs},
    Title = {Org-mode Manual},}

Here notice the first keywords is the directory structure I want to have.
Then I set up a template of autofile, (%k[/]1/%l%n0%e), telling BibDesk to
"Build the directory structure based on my first keyword and rename it as
what I want, then check it in".
To me, this workflow for organizing digital references is complete now.

 I do think that BibDesk has great features to investigate, such as create
the record from the bibtex and embed the picture inside the bibtex itself.
Maybe we could also use the *.org as a database file and develop a framework
to have our entries displayed in more intuitive way, maybe by using smart
group, tag(keywords).

Sorry for this such a long post, and looking forward to comments.

Best,

Chao

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Re: Academic Reference Workflows and recommendation of Bibdesk

[Matt Lundin]

Chao LU <loochao@gmail.com> writes:

> First of all it's free, open resource. Its database file is just an
> bibtex file, so all the records is in plain text, even the thumbnails
> are stored inside this bibtex file. like below,
>
> I do think that BibDesk has great features to investigate, such as
> create the record from the bibtex and embed the picture inside the
> bibtex itself.

Eric Schulte recently added some nice features to org-bibtex.el that
allow for easy entry of bibliographical data in an org file (and export
to bibtex). For instance, one can now import bibtex fields as org
properties.

> Maybe we could also use the *.org as a database file and develop a
> framework to have our entries displayed in more intuitive way, maybe
> by using smart group, tag(keywords).

Would a sparse tree or tags view suffice here, or do you have something
else in mind?

Best,
Matt

Re: Academic Reference Workflows and recommendation of Bibdesk

[Christian Moe]

On 6/4/11 12:54 AM, Chao LU wrote:
> Dear All,
>
> Here I'd like to discuss my workflow for Academic reference and
> recommend you Bibdesk.
>
> I use iTune to manage all my mp3 files. Mp3 format has the ability to
> store all the metadata into the file itself, and iTune offers a way to
> modify and display certain kind of music according to the metadata.
> Inspired by this, I was looking for similar way to organize all the
> academic references and even to build a personal digital library. I've
> tried a lot of softwares, Mendeley, Zotero, Papers, Endnote, Org-mode,
> Yep, BibDesk...
>
> My feeling is that, Org could get this done, but BibDesk does a better
> job.

Then you should probably use BibDesk? It depends on whether it's more 
important for you to use the best tool for each part of the job, or to 
do as many parts of the job as possible in the same Org environment. 
If the job is managing references, then the best tool is likely to be 
a dedicated reference manager.

Org-mode has ample general-purpose functionality that can be used to 
manage academic references (and recent changes to org-bibtex have made 
this option more attractive). But it was not designed as a dedicated 
tool for this purpose.

Org-mode integrates quite smoothly with BibTeX, and it can be 
integrated with stand-alone reference managers (I don't have an 
overview, but I know about various partial solutions for Zotero, such 
as Fireforg and Erik Hetzner's Zotero-plain).

> To check in an entry such as "org-manual-7.5.pdf" to the library, one
> could do:
>
> Library.org
> ---------------------------------------------
> #+LINK: pdf file:./Emacs/%s.pdf
> #+LINK: txt file:./Emacs/%s.txt
  (...snip...)
> Location: [[pdf:org-manual-7.5]]
> --------------------------------------------
> Then use org-attach to get the file settle down in the right place.
>

It seems superfluous to define two different link types for pdf and 
text files when the links don't do anything differently and don't save 
typing.

And if you have archived the file, then the link is in principle 
superfluous (especially if you have one attachment per ID'd entry), 
since you can open the current entry's attachment(s) with `C-c C-a o'.

> However this process is quite time consuming, and non-intuitive. I
> prefer the features provided in iTune, Papers2, Bibtex, which could
> provide thumbnail and quicklooks of the files.

Those are two different issues.

> *2. the Bibdesk way:*
> Now I'd like to recommend BibDesk here.
>
> First of all it's free, open resource. Its database file is just an
> bibtex file, so all the records is in plain text, even the thumbnails
> are stored inside this bibtex file. like below,
> =======================
> Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gk....(It's
> very long png source code, so I abridged here)}
> =======================
>
> Second, Bibdesk has a much more intuitive UI, and thumbnails are
> provided. It also support keywords, smart groups...

Tags?

> Moreover, Bibdesk has a great feature called autofile, which could
> attach the file to certain directories (and build the directories
> structures you want as well!) Here is the example:

In Org, you can specify the attachment directory of your choice in the 
ATTACH_DIR property of the entry. If the path does not exist, it will 
be created when an attachment is made. You can set the ATTACH_DIR 
property with `C-c C-a s'. This seems to do everything the autofile 
feature you describe can do, perhaps at the expense of a couple of 
extra keystrokes of typing per entry.

>
>   I do think that BibDesk has great features to investigate, such as
> create the record from the bibtex and embed the picture inside the
> bibtex itself.

As Matt Lundin already mentioned, Eric Schulte has recently provided a 
user-friendly way to convert between BibTeX and Org records. See 
org-bibtex.el in the development version or

https://github.com/eschulte/org-bibtex/blob/master/org-bibtex.el

If you need thumbnails, someone could probably cobble up a way to add 
them with, say, ImageMagick (for PDFs at least; and for .txt or .html 
documents, maybe text excerpts would be just as helpful?).


But if you like both Bibdesk and Org-mode, the more interesting 
question is probably how you can integrate the two.

Yours,
Christian

Re: Academic Reference Workflows and recommendation of Bibdesk

[Eric Schulte]

>
> As Matt Lundin already mentioned, Eric Schulte has recently provided a
> user-friendly way to convert between BibTeX and Org records. See
> org-bibtex.el in the development version or
>
> https://github.com/eschulte/org-bibtex/blob/master/org-bibtex.el
>

This functionality has now been moved into the core of Org-mode, so if
you are running the latest Org-mode these bibtex functions are already
loaded on your system, simply tab complete function names starting with
"org-bibtex-" to see the available options.

Best -- Eric

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/