From mboxrd@z Thu Jan 1 00:00:00 1970 From: Chao LU Subject: Academic Reference Workflows and recommendation of Bibdesk Date: Fri, 3 Jun 2011 18:54:29 -0400 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=00151747ba960d50d404a4d6a449 Return-path: Received: from eggs.gnu.org ([140.186.70.92]:56409) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QSdGX-00020W-CJ for emacs-orgmode@gnu.org; Fri, 03 Jun 2011 18:54:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1QSdGV-0004eS-EZ for emacs-orgmode@gnu.org; Fri, 03 Jun 2011 18:54:53 -0400 Received: from mail-fx0-f41.google.com ([209.85.161.41]:62745) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1QSdGU-0004eL-SX for emacs-orgmode@gnu.org; Fri, 03 Jun 2011 18:54:51 -0400 Received: by fxm18 with SMTP id 18so1971800fxm.0 for ; Fri, 03 Jun 2011 15:54:49 -0700 (PDT) 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: emacs-orgmode@gnu.org --00151747ba960d50d404a4d6a449 Content-Type: text/plain; charset=ISO-8859-1 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 --00151747ba960d50d404a4d6a449 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

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

I use iTune to manage all my mp3 f= iles. Mp3 format has the ability to store all the metadata into the file it= self, and iTune offers a way to modify and display certain kind of music ac= cording 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, Endno= te, 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
`--- Cultur= e/
`--- Mathematics/
`--- Unix/
=A0=A0=A0=A0=A0 `-----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<= br>** Org-mode
***=A0 Manual of version 7.5=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 :Emacs:Org:Manual:
:PROPRIETIES:
:Title:
:Author:
:Subject:
:Keywords:
:Comment= s:
: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-agend= a files, then define a related org-agenda command. (It's kind like the = smart group concept in iTune)

However this process is quite time con= suming, 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 her= e.

First of all it's free, open resource. Its database file is j= ust an bibtex file, so all the records is in plain text, even the thumbnail= s are stored inside this bibtex file. like below,
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Bd= sk-File-1 =3D {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gk....(It's ve= ry long png source code, so I abridged here)}
=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

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

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

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

I just have this Bibtex entry ready:

@article{OrgManual:7.5,
= =A0=A0=A0 Author =3D {Org-Mode},
=A0=A0=A0 Date-Added =3D {2011-06-03 16= :07:44 -0400},
=A0=A0=A0 Date-Modified =3D {2011-06-03 16:14:54 -0400},<= br>=A0=A0=A0 Keywords =3D {/Unix/Emacs,=A0 Emacs},
=A0=A0=A0 Title =3D {Org-mode Manual},}

Here notice the first keywor= ds is the directory structure I want to have.
Then I set up a template o= f 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 chec= k it in".
To me, this workflow for organizing digital references is complete now.
=
=A0I do think that BibDesk has great features to investigate, such as c= reate the record from the bibtex and embed the picture inside the bibtex it= self. Maybe we could also use the *.org as a database file and develop a fr= amework 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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