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Re: [O] Academic Reference Workflows and recommendation of Bibdesk

From: Christian Moe
Subject: Re: [O] Academic Reference Workflows and recommendation of Bibdesk
Date: Sun, 05 Jun 2011 17:47:43 +0200
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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

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:

#+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 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...


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.


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