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#+title: Bog
#+options: toc:nil
#+startup: showall

[[https://travis-ci.org/kyleam/bog][https://travis-ci.org/kyleam/bog.svg]]

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

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).

#+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. 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 (usually a PDF) 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 (usually a PDF) to be associated with a citekey.

- =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=
- =bog-insert-heading-citekey=
- =bog-open-first-citekey-link=

* 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.

* Other approaches

If Bog doesn't fit your workflow, there are a good number of other
approaches to explore. On the Org mode mailing list, there are some [[http://thread.gmane.org/gmane.emacs.orgmode/78983][nice]]
[[http://thread.gmane.org/gmane.emacs.orgmode/14756][descriptions]] of systems people have come up with for taking research
notes in Org. For a package that focuses on both taking research notes
and writing research articles, look into [[https://github.com/jkitchin/jmax/blob/master/org/org-ref.org][Org-ref]].