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

[Eric Schulte]

Ian Barton <address@hidden> 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.
>>
>
> Can't help with managing the citations in org, as the last time I had
> to do this I was using a card index file:)
>
> However, to address your other questions one way of doing this would
> be to create an org file with a heading for each article:
>
> * Article 1.
> Here are some notes.
>
> * Article 2
> My notes
>

I've been using such an org file for most of grad school and I couldn't
be happier with the results.  I have a single reading.org file with one
top-level entry for each article I read.  Currently at 533 articles
(many still tagged TODO) and 16,558 lines.

To create each headline, I first copy the bibtex information onto my
clipboard, then I call `org-bibtex-yank' which converts the bibtex
information into a headline with properties. E.g.,

    * Software mutational robustness
      :PROPERTIES:
      :TITLE:    Software mutational robustness
      :BTYPE:    article
      :CUSTOM_ID: schulte2013software
      :YEAR:     2013
      :ISSN:     1389-2576
      :JOURNAL:  Genetic Programming and Evolvable Machines
      :DOI:      10.1007/s10710-013-9195-8
      :URL:      http://dx.doi.org/10.1007/s10710-013-9195-8
      :PUBLISHER: Springer US
      :KEYWORDS: Mutational robustness; Genetic programming; Mutation testing; 
Proactive diversity; N-version programming; Neutral landscapes
      :AUTHOR:   Schulte, Eric and Fry, ZacharyP. and Fast, Ethan and Weimer, 
Westley and Forrest, Stephanie
      :PAGES:    1-32
      :LANGUAGE: English
      :END:
    file:papers/10.1007_s10710-013-9195-8.pdf

    The arXiv preprint is up at http://arxiv.org/abs/1204.4224.

    More notes...

>
> You can create hyperlinks to each article from org. See
> http://orgmode.org/org.html#Hyperlinks for more detailed information.
>

This is handy, I start every entry with a hyperlink to the pdf file.

>
> However, you should perhaps decide first how you might structure your
> org file. You might want to group articles under an author heading, or
> perhaps more likely by subject area, with a sub heading for each
> article under the main heading.
>

Personally I'm a fan of the flat file organization.  Whenever I want to
find a particular paper I just search for the first string that comes to
mind.

>
> You may also want to tag each article. See
> http://orgmode.org/org.html#Tags Org lets you quickly narrow your view
> of an org file so that you are only seeing headings with specific
> tags.
>

This is a good idea.  I've not used tags much previously but it looks
like Org-mode has wonderful tag search functionality.  I wonder if
there's an easy way to automatically include the content of the
:KEYWORDS: property in tag searches.

Best,

>
> Ian.
>
>
>

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D