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#+title: Bog

Bog is a system for taking research notes in [[http://orgmode.org/][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.

* 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 [[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 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, but it shouldn't be so easy that I file them away
   without giving them any thought. For me, this means glancing over it
   at least enough to place it under a general topic (or capturing the
   article and a link in my normal Org notes system until I take time to
   refile it to my research notes). I only retrieve the BibTeX file or
   PDF file when I need to use them.

* Features

** 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.

#+begin_example
  # In a very general topic file

  ,* Topic heder

  ,** name2000word                                    :atag:

  <URL for study>

  Article notes
#+end_example

"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.

#+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

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.

** Referencing studies within notes

You can reference other studies with their citekey.

#+begin_example
  ,** name2000word                                    :atag:

  Another study (another1999word).
#+end_example

"another1999word" will be highlighted within the text. When the point is
within the citekey, many Bog functions can extract and use the citekey.

** 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.

** 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 [[Opening%20a%20PDF%20file][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

** 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.

** 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%20a%20PDF%20file][Opening a PDF file]].)

** 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.

** 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.

* 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.

#+begin_src emacs-lisp
  (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)
#+end_src