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_____
BOG
_____
Table of Contents
_________________
1 Bog workflow
2 Features
.. 2.1 Adding citekeys to notes
.. 2.2 Referencing studies within notes
.. 2.3 Opening a PDF file for a citekey
.. 2.4 Opening a BibTeX file for a citekey
.. 2.5 Searching online for a citekey
.. 2.6 Renaming a new PDF
.. 2.7 Renaming a new BibTeX file
.. 2.8 Generating a combined BibTeX file
3 Recommended keybindings
Bog is a system for taking research notes in [Org mode]. As any Org user
knows, Org handles notetaking beautifully. Bog just adds a few
research-specific features, nearly all of which are focused on managing
and taking notes with Org, not on writing research articles with Org.
[Org mode] http://orgmode.org/
1 Bog workflow
==============
Many people use Org for taking research notes, and there are some
really nice descriptions of systems people have come up with (for a
few examples, see [these] [threads] on the Org mode mailing list).
The workflow for Bog is based on these preferences:
1. I don't want to store a lot of metadata with my notes.
The citekey is the unique identifier that I use to link the notes
with the BibTeX and PDF files. With just the citekey, I should be
able to access this. If desired, more information can be added
(such as bibliographic properties that can be generated with
org-bibtex), but this is not required.
One of the reasons for this is #2.
2. I want to have low friction for adding articles to the notes, but
not mindless.
There is an endless stream of research articles, so it should be
easy to add them. On the other hand, it shouldn't be so easy that I
file them away without giving them any thought. For me, this means
capturing the article and a link in my normal Org notes system. At
some point, I glance over it enough to decide what general topic it
should be in and refile it into a research notes file.
I prefer adding BibTeX and PDF files lazily. My only requirement is
that I put it in a relevant heading and that I name it with a
proper citekey. I make sure to add a link to the study online. I
only retrieve the BibTeX file or PDF file when I need to use them.
[these] http://thread.gmane.org/gmane.emacs.orgmode/78983
[threads] http://thread.gmane.org/gmane.emacs.orgmode/14756
2 Features
==========
2.1 Adding citekeys to notes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
As mentioned above, when citekeys are added, they should be filed
under the appropriate topic. I organize my research notes into a few
files with broad topics then have one level of headers representing
topics to file studies under.
,----
| # In a very general topic file
|
| * Topic heder
|
| ** name2000word :atag:
|
| <URL for study>
|
| Article notes
`----
"name2000word" is the study header. Bog expects the study citekey to
be the title or property of a heading.
The default format for the citekey is the first author's last name,
the year, and then the first non-trivial word. To have BibTeX mode
automatically generate a key of this format, the `bibtex-autokey-*'
settings can be modified.
,----
| (setq bibtex-autokey-year-length 4
| bibtex-autokey-titleword-length nil
| bibtex-autokey-titlewords-stretch 0
| bibtex-autokey-titlewords 1
| bibtex-autokey-year-title-separator "")
`----
If the study was added when checking journals online, I tend to add
the URL right under the heading. However, I often add citekeys from
the references of an article that I'm reading. In this case, I often
store only the heading.
2.2 Referencing studies within notes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can reference other studies with their citekey.
,----
| ** name2000word :atag:
|
| Another study (another1999word).
`----
"another1999word" will be highlighted within the text. When the point
is within the citekey, many Bog functions can extract and use the
citekey.
2.3 Opening a PDF file for a citekey
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
All PDF files are kept in a single directory and are named as
<citekey>-*.pdf. The function `bog-find-citekey-pdf' will open a PDF
associated with a citekey. If the point is on a citekey, it will open
that citekey. Otherwise, it will use the citekey from the first parent
heading that is a study.
2.4 Opening a BibTeX file for a citekey
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The function `bog-find-citekey-bib' will open the BibTeX entry
associated with a citekey.
The citekey is obtained in the same way as the PDF citekey.
BibTeX entries can be stored in one of two ways:
1. As a single file with many entries
2. As single-entry files named <citekey>.bib within a common directory
2.5 Searching online for a citekey
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The function `bog-search-citekey-on-web' will perform a search with
the citekey information. By default, Google Scholar is searched. The
default citekey format (first author's last name, year, and first
non-trivial word) usually contains enough information to make this
search successful.
2.6 Renaming a new PDF
~~~~~~~~~~~~~~~~~~~~~~
New PDF files can be put in a "stage" directory and then renamed to a
citekey. (The citekey can be taken from the notes context, as
described in Opening a PDF file.)
2.7 Renaming a new BibTeX file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If a separate BibTeX file is used for each citekey,
`bog-rename-and-clean-new-bib-files' can be used to rename all new
BibTeX files. `bibtex-clean-entry' is used to clean the entry and
autogenerate the key.
2.8 Generating a combined BibTeX file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If single-entry BibTeX files are used, there should be a way to
collect the references that are needed. `bog-create-combined-bib' can
be used to create a BibTeX file that has entries for all the citekeys
in the current buffer.
3 Recommended keybindings
=========================
Bog doesn't claim any keybindings, but using "C-c b" as a prefix while
in Org mode is a good option.
Key Command
------------------------------------
C-c b p bog-find-citekey-pdf
C-c b b bog-find-citekey-bib
C-c b w bog-search-citekey-on-web
This can be achieved by placing the code below in your .emacs file.
,----
| (define-prefix-command 'bog-map)
| (define-key org-mode-map (kbd "C-c b") 'bog-map)
| (define-key bog-map "p" 'bog-find-citekey-pdf)
| (define-key bog-map "b" 'bog-find-citekey-bib)
| (define-key bog-map "w" 'bog-search-citekey-on-web)
`----
|