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<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Workflow</a></li>
<li><a href="#sec-2">2. Main features</a>
<ul>
<li><a href="#sec-2-1">2.1. Opening a PDF file for a citekey</a></li>
<li><a href="#sec-2-2">2.2. Opening a BibTeX file for a citekey</a></li>
<li><a href="#sec-2-3">2.3. Searching online for a citekey</a></li>
<li><a href="#sec-2-4">2.4. Renaming new PDFs</a></li>
<li><a href="#sec-2-5">2.5. Renaming new BibTeX files</a></li>
<li><a href="#sec-2-6">2.6. Generating a combined BibTeX file</a></li>
</ul>
</li>
<li><a href="#sec-3">3. Variables</a></li>
<li><a href="#sec-4">4. Recommended keybindings</a></li>
</ul>
</div>
</div>
Bog is a system for taking research notes in [Org mode](http://orgmode.org/). It 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.
# 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](http://thread.gmane.org/gmane.emacs.orgmode/78983) [threads](http://thread.gmane.org/gmane.emacs.orgmode/14756) on the Org mode mailing list).
The Bog workflow is focused around the citekey, which is the only study
information that must be included in the notes. This unique identifier
is used as a link to the BibTeX and PDF files.
In the example below, the citekey "name2000word" is a study heading. Bog
expects the citekey to be the title or property of a heading. The
citekey "another1999study" is a reference to another study (which may or
may not have a subtree in this or another Org file).
* Topic heading
** TODO name2000word :atag:
<URL for study>
Article notes ... a reference to another1999study ...
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 "")
# Main features
Many Bog functions take the citekey from the notes context. If the point
is on a citekey (like "another1999study" above), then that citekey will
be used. Otherwise, the citekey will be taken from the first parent
heading that is a study. If one isn't found, the user will be prompted
for the citekey.
## Opening a PDF file for a citekey
The function `bog-find-citekey-pdf` will open a PDF associated with a
citekey.
## Opening a BibTeX file for a citekey
The function `bog-find-citekey-bib` will open the BibTeX entry
associated with a 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
## Searching online for a citekey
The function `bog-search-citekey-on-web` will perform a Google Scholar
search with the citekey information. The default citekey format (first
author's last name, year, and first non-trivial word) usually contains
enough information to make this search successful.
## Renaming new PDFs
New PDF files can be put in a "stage" directory and then renamed to a
citekey.
## Renaming new BibTeX files
If a separate BibTeX file is used for each citekey,
`bog-clean-and-rename-staged-bibs` can be used to rename all new BibTeX
files. `bibtex-clean-entry` is used to clean the entry and autogenerate
the key.
## 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.
# Variables
Several variables determine where Bog looks for things.
- bog-notes-directory
- bog-pdf-directory
- bog-bib-directory or bog-bib-file
- bog-stage-directory
The variables below are important for specifying how Bog behaves.
- **bog-citekey-format:** A regular expression that defines the format
used for citekeys
- **bog-citekey-func:** A function to extract a citekey from the current
subtree. Use this to indicate whether the citekey should be taken
from the heading or property.
- **bog-find-citekey-bib-func:** A function to find a citekey in a BibTeX
file. This determines whether a directory of single-entry BibTeX
files or a single BibTeX file is used.
# Recommended keybindings
Bog doesn't claim any keybindings, but using "C-c b" as a prefix while
in Org mode is a good option.
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="left" />
<col class="left" />
</colgroup>
<thead>
<tr>
<th scope="col" class="left">Key</th>
<th scope="col" class="left">Command</th>
</tr>
</thead>
<tbody>
<tr>
<td class="left">C-c b p</td>
<td class="left">bog-find-citekey-pdf</td>
</tr>
<tr>
<td class="left">C-c b r</td>
<td class="left">bog-rename-staged-pdf-to-citekey</td>
</tr>
<tr>
<td class="left">C-c b b</td>
<td class="left">bog-find-citekey-bib</td>
</tr>
<tr>
<td class="left">C-c b h</td>
<td class="left">bog-goto-citekey-heading-in-buffer</td>
</tr>
<tr>
<td class="left">C-c b H</td>
<td class="left">bog-goto-citekey-heading-in-notes</td>
</tr>
<tr>
<td class="left">C-c b w</td>
<td class="left">bog-search-citekey-on-web</td>
</tr>
</tbody>
</table>
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 "r" 'bog-rename-staged-pdf-to-citekey)
(define-key bog-map "b" 'bog-find-citekey-bib)
(define-key bog-map "h" 'bog-goto-citekey-heading-in-buffer)
(define-key bog-map "H" 'bog-goto-citekey-heading-in-notes)
(define-key bog-map "w" 'bog-search-citekey-on-web)
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