From: Eric Schulte <schulte.eric@gmail.com>
To: Richard Lawrence <richard.lawrence@berkeley.edu>
Cc: emacs-orgmode@gnu.org
Subject: Re: managing articles in my personal library, and their citational material, using org mode instead of bibtex
Date: Thu, 21 Nov 2013 15:00:00 -0700 [thread overview]
Message-ID: <87fvqpza8v.fsf@gmail.com> (raw)
In-Reply-To: <87ob5fgglx.fsf@berkeley.edu> (Richard Lawrence's message of "Wed, 20 Nov 2013 08:52:58 -0800")
Richard Lawrence <richard.lawrence@berkeley.edu> writes:
> Eric Schulte <schulte.eric@gmail.com> writes:
>
>> Ian Barton <lists@wilkesley.net> writes:
>>
>>> On 19/11/13 01:40, Christopher W. Ryan wrote:
>>>> Not sure "citational" is even a word, but hopefully it conveys my meaning!
>>>>
>>>> I've been using LaTeX for academic writing and reading for quite some
>>>> time, with emacs as my editor. I'm pretty familiar with managing a .bib
>>>> file containing all the references I've collected, and using it in LaTeX
>>>> \cite commands.
>>>>
>>>> I've come to org-mode more recently. I'm trying to imagine how I might
>>>> use it to manage my "personal library." I have a directory full of pdf
>>>> files, each a downloaded article. Some articles I reference in papers I
>>>> write; others I just read and want to keep. I also have a .bib file
>>>> where I put the citational material for all those articles. Whenever I
>>>> download an article, I add its entry to my .bib file. I tend to manage
>>>> this with JabRef because it searches Medline so easily, but I also will
>>>> edit the .bib file directly when necessary.
>>>>
>>>> I like the idea of an org file containing the citational information
>>>> (authors, title, journal, etc) *plus* links to the pdfs on my hard
>>>> drive, or on the internet. I could also include my notes about the
>>>> articles. But what would that org file look like? How do I insert a
>>>> reference to an article into the org file which contains the article I
>>>> am writing?
>>>>
>>>> I'd be grateful for any explanations, or links to tutorials.
>>>>
>
> I am also a grad student, and I use a setup which is similar to Eric's,
> but rather than importing from bibtex, I use Org's capture features to
> directly input the bibliographic data when I come across something I
> want to add to my reading list. I don't maintain a separate .bib file
> at all; rather I generate it as needed from the Org file containing my
> reading list.
>
> This setup allows me to think of readings as TODO items included in my
> agenda, take notes and make links in the entry, and also keep
> bibliographic data in Org (which I export via org-bibtex).
>
> Here's what my setup looks like:
>
> 1) A capture template for new readings. My template looks like this:
>
> ** %^{Todo state|FIND|PRINT|READ|NOTES} [#%^{Priority|A|B|C}] %^{Description|Reading} %^g
> %^{TITLE}p %^{AUTHOR}p %^{AREA}p %?
> :PROPERTIES:
> :Entered: %U
> :END:
>
> This template does not have a field for adding links to PDFs, but you
> could easily add that.
>
> 2) A hook to add bibliographic data to reading entries when finalizing a
> capture. I put this in my Org setup:
>
> ;; post-processing in capture templates
> (defun add-bibliographic-data ()
> ; this is a bit hacky: we detect the AUTHOR property, and create bibtex entries if
> ; it is present
> (message "optionally adding bibliographic data")
> (if (and (org-entry-get (point) "AUTHOR")
> (y-or-n-p "Add bibliographic data? "))
> ; with prefix arg to get all fields:
> (org-bibtex-create-in-current-entry 1)
> nil))
>
> (add-hook 'org-capture-before-finalize-hook (lambda () (add-bibliographic-data)))
>
> There may be a better way to do this, but it works for me!
>
> 3) Elisp functions to export my entire reading list to .bib (these
> assume that your readings are not in a separate file, but under a top-level
> entry called "Reading list" in some other file):
>
> ;; lib/el/bib-export.el in my dissertation tree:
> (setq dissertation-bib-file "~/Documents/philosophy/dissertation/build/dissertation.bib")
>
> (defun add-headline-to-bib-buffer (bib-buffer)
> "Export headline at point to Bibtex into the given buffer"
> (let ((bib-entry (org-bibtex-headline))
> (custom-id (org-entry-get (point) "CUSTOM_ID")))
> (if (and custom-id bib-entry)
> (with-current-buffer bib-buffer
> (insert bib-entry)))))
>
> (defun export-subtree-to-bib-buffer (headline bib-buffer)
> "Export the entries in the subtree at point to Bibtex into the given buffer."
> (save-excursion
> (goto-char (org-find-exact-headline-in-buffer headline))
> (org-map-entries
> (lambda () (add-headline-to-bib-buffer bib-buffer))
> t ; match: all entries below this one
> 'tree ; scope: just this subtree
> )))
>
> (defun reading-list-to-bibtex ()
> "Export 'Reading list' headline in current buffer to dissertation.bib"
> (interactive)
> (let ((org-buffer (current-buffer))
> (bib-buffer (create-file-buffer "dissertation.bib")))
> (export-subtree-to-bib-buffer "Reading list" bib-buffer)
> (with-current-buffer bib-buffer
> (write-file dissertation-bib-file))))
>
> 4) A Makefile entry to call the export functions:
>
> BATCH_EMACS=$(EMACS) --batch -Q
>
> bib: tasks.org lib/el/bib-export.el
> $(BATCH_EMACS) --load lib/el/bib-export.el --file tasks.org --funcall reading-list-to-bibtex
>
>
> Thus, I can run "make bib" in my dissertation tree and get a fresh
> export of all my readings to a .bib file.
>
> Hope that helps!
>
> Best,
> Richard
>
Very cool,
I think some of these functions could be merged into
contrib/lisp/org-bibtex-extras.el to very good effect. In the mean time
I just pushed up a small change to this file which will resolve cite:
links and export them correctly to LaTeX.
Cheers,
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
next prev parent reply other threads:[~2013-11-21 22:01 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-11-19 1:40 managing articles in my personal library, and their citational material, using org mode instead of bibtex Christopher W. Ryan
2013-11-19 8:28 ` Ian Barton
2013-11-19 16:25 ` Eric Schulte
2013-11-20 2:48 ` Alan L Tyree
2013-11-20 3:37 ` Eric Schulte
2013-11-20 6:16 ` Alan L Tyree
2013-11-20 6:27 ` Jambunathan K
2013-11-21 21:14 ` Alan L Tyree
2013-11-22 4:04 ` Eric Schulte
2013-11-22 5:37 ` Alan L Tyree
2013-11-25 10:06 ` Jambunathan K
2013-11-20 16:52 ` Richard Lawrence
2013-11-21 22:00 ` Eric Schulte [this message]
2013-11-22 4:03 ` Eric Schulte
2013-11-23 0:06 ` Richard Lawrence
2013-11-19 10:41 ` Karl Voit
2013-11-25 18:29 ` John Kitchin
-- strict thread matches above, loose matches on Subject: below --
2013-11-21 0:49 Jorge A. Alfaro Murillo
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