# -*- mode: org -*-
#+title: Bog
#+options: toc:nil
#+startup: showall

Bog is a system for taking research notes in [[http://orgmode.org/][Org mode]]. 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 [[http://melpa.milkbox.net/][MELPA]].

To enable Bog in all Org buffers, add it to =org-mode-hook=.

#+begin_src emacs-lisp
  (add-hook 'org-mode-hook 'bog-mode)
#+end_src

* 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 [[http://thread.gmane.org/gmane.emacs.orgmode/78983][these]] [[http://thread.gmane.org/gmane.emacs.orgmode/14756][threads]] 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. 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).

#+begin_example

  ,* Topic heading

  ,** TODO name2000word                               :atag:

  <URL for study>

  Article notes ... a reference to another1999study ...
#+end_example

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.

#+begin_src emacs-lisp
  (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 "")
#+end_src

* 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.

- =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-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-citekey-function=

  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-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=.