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From: Christian Moe <mail@christianmoe.com>
To: Chao LU <loochao@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: Academic Reference Workflows and recommendation of Bibdesk
Date: Sun, 05 Jun 2011 17:47:43 +0200	[thread overview]
Message-ID: <4DEBA51F.4050500@christianmoe.com> (raw)
In-Reply-To: <BANLkTi=iCEKMNKEMkc42m4-O=y9w=eHBiA@mail.gmail.com>

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
> 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 

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...


> 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


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.


  parent reply	other threads:[~2011-06-05 15:47 UTC|newest]

Thread overview: 4+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2011-06-03 22:54 Academic Reference Workflows and recommendation of Bibdesk Chao LU
2011-06-04 13:15 ` Matt Lundin
2011-06-05 15:47 ` Christian Moe [this message]
2011-06-05 16:05   ` Eric Schulte

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