From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christian Moe Subject: Re: Academic Reference Workflows and recommendation of Bibdesk Date: Sun, 05 Jun 2011 17:47:43 +0200 Message-ID: <4DEBA51F.4050500@christianmoe.com> References: Reply-To: mail@christianmoe.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:54203) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QTFY7-0007l4-L6 for emacs-orgmode@gnu.org; Sun, 05 Jun 2011 11:47:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1QTFY5-0003Au-Gm for emacs-orgmode@gnu.org; Sun, 05 Jun 2011 11:47:35 -0400 Received: from mars.hitrost.net ([91.185.211.18]:42559) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QTFY4-0002gP-W6 for emacs-orgmode@gnu.org; Sun, 05 Jun 2011 11:47:33 -0400 In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Chao LU Cc: emacs-orgmode@gnu.org 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