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

[Alan L Tyree <alantyree@gmail.com>]

On 20/11/13 14:37, Eric Schulte wrote:
> Alan L Tyree <alantyree@gmail.com> writes:
>
>> On 20/11/13 03:25, Eric Schulte wrote:
>>> 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.
>>>>>
>>>> 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...
>>>
>> Is there some easy way to import entire bibtex files in this way?
>>
> org-bibtex-import-from-file
>
>> I find citations to be frustrating. Is there some way that bibtex (or
>> org files such as the above) can be used to enter citations in an org
>> file so that they are exported correctly by the different exporters?
>>
>> Or is there someplace where all this information is gathered and I
>> just am too blind to see it?
>>
> I don't know, I personally use org-bibtex-export-to-kill-ring to convert
> citations to bibtex individually and manually.
I think I have a terminology problem. What I mean is to enter something 
like \cite{mann82} in the text and have it spit out (Mann 1982) in each 
and every export as well as constructing an entry for the bibliography.

Of course, the actual form of the output should be configurable to some 
extent, but I'd be happy with one form that always comes out the same.

Is that possible? I'm currently fudging the issue by entering a Markdown 
style entry in the text, for example [@mann82:_legal_aspec_money], 
exporting to Markdown and then using Pandoc to get the final result.

Not elegant.

Cheers,
Alan

>> Thanks for any help.
>> Alan
>>
>> <SNIP>


-- 
Alan L Tyree                    http://www2.austlii.edu.au/~alan
Tel:  04 2748 6206              sip:typhoon@iptel.org