Re: managing articles in my personal library, and their citational material, using org mode instead of bibtex

[John Kitchin <jkitchin@andrew.cmu.edu>]

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I have the following org/bibtex habits:

1. I keep all bibtex entries in a single bibtex file, usually by pasting
them from one source to the file. I save the pdf of the article with a
filename equal to the bibtex key in a single directory.

With the point on the bibtex entry, I run a command defined here (
https://github.com/jkitchin/jmax/blob/prelude/jorg-bib.el#L76) that creates
a TODO entry in my notes.org file with a link to the pdf file in it. I can
run another command that opens the pdf file. I bind those commands to f11
and f12 for convenience. For a while, I also had the entry automatically
added to citeulike. Here is an example entry in my notes.org file. These
TODO get picked up in my agenda to remind me to read them.

** TODO 2005 - {A general scheme for the estimation of oxygen  binding
energies on binary transition metal surface  alloys}
 :PROPERTIES:
  :Custom_ID: Greeley2005
  :AUTHOR: Greeley, Jeff and N{\o}rskov, Jens K.
  :JOURNAL: Surface Science
  :YEAR: 2005
  :VOLUME: 592
  :PAGES: 104--111
 :END:
[[cite:Greeley2005]]
[[file:~/Dropbox/bibliography/bibtex-pdfs/Greeley2005.pdf][pdf]]

in my jorg-bib.el file I define a lot of cite links. These let me click on
a key in a cite:key1,key2  link and open the entry in the bibtex file, i.e.
if I click on key1 it goes to that entry, and if I click on key2 it goes to
that entry. Once I could right click on a key and open the pdf, but I seem
to have misplaced that function, now I just click the link which opens the
bibtex file at the entry, and I press f12 which opens the pdf. I find this
clicking to get the full entry very handy when I am working on manuscripts
and trying to remember what I cited.

The links get converted to \cite{} for latex. I do not have a good html
solution yet, mostly because I don't need it that often. I haven't tried
the org-bibtex code yet, and don't have bibtex2html on my windows machine.

This "mostly" works fine for me, and suits my workflows.

John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Mon, Nov 18, 2013 at 8:40 PM, Christopher W. Ryan
<cryan@binghamton.edu>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.
>
> Thanks.
>
> --Chris Ryan
> SUNY Upstate Medical University
> Binghamton, NY
>
>

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