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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.
# Installation
Bog is available on [MELPA](http://melpa.milkbox.net/).
To enable Bog in all Org buffers, add it to `org-mode-hook`.
(add-hook 'org-mode-hook 'bog-mode)
# 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 file and other associated files.
In the example below, the citekey "name2000word" is a study heading. A
study heading is defined as a heading the has a citekey as a title or as
the value of `bog-citekey-property`. When a citekey occurs anywhere else
(like "another1999study" below), they are taken as 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. If the point is on a
citekey (like "another1999study" above), then that citekey will be used.
If this fails, many functions will try to take the citekey from the
first parent heading that is a study heading.
- `bog-find-citekey-file`
Open an associated file for a citekey.
- `bog-find-citekey-bib`
Open a BibTeX file for a citekey.
BibTeX entries can be stored in one of two ways:
- As a single file with many entries
- As single-entry files named citekey.bib within a common directory
- `bog-search-citekey-on-web`
Search Google Scholar for a citekey. The default citekey format (first
author's last name, year, and first non-trivial word) usually contains
enough information to make this search successful.
- `bog-rename-staged-file-to-citekey`
Rename a new file.
- `bog-clean-and-rename-staged-bibs`
Rename new BibTeX files. If a separate BibTeX file is used for each
citekey, this function can be used to rename all new BibTeX files.
`bibtex-clean-entry` is used to clean the entry and autogenerate the
key.
- `bog-create-combined-bib`
Generate a combined BibTeX file for all citekeys in buffer. This is
useful if single-entry BibTeX files are used.
Other useful functions include
- `bog-goto-citekey-heading-in-buffer`
- `bog-goto-citekey-heading-in-notes`
- `bog-citekey-tree-to-indirect-buffer`
- `bog-refile`
- `bog-search-notes`
- `bog-search-notes-for-citekey`
- `bog-sort-topic-headings-in-buffer`
- `bog-sort-topic-headings-in-notes`
# Variables
Several variables determine where Bog looks for things.
- `bog-notes-directory`
- `bog-file-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-find-citekey-bib-function`
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.
# Keybindings
A keymap is defined for Bog under the prefix `C-c "`. If you prefer
something else (like `C-c b`), set `bog-keymap-prefix`.
Some Bog functions are useful outside of an Org buffer (e.g.,
`bog-search-notes`). These functions are available through the
`bog-commander` interface (based of off `projectile-commander`). This
can be bound to a global key for quick access.
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