Bog

Bog is a system for taking research notes in 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 MELPA.

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

(add-hook 'org-mode-hook #'bog-mode)

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 that has a citekey as a title or as the value of bog-citekey-property. When a citekey occurs anywhere else (like “another1999study” below), it is 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 'infty
      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 (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-citekey-tree-to-indirect-buffer
• bog-goto-citekey-heading-in-notes
• bog-insert-heading-citekey
• bog-jump-to-topic-heading
• bog-list-duplicate-heading-citekeys
• bog-list-orphan-citekeys
• bog-open-citekey-link
• bog-open-first-citekey-link
• bog-refile
• bog-search-notes
• bog-search-notes-for-citekey
• bog-sort-topic-headings-in-buffer
• bog-sort-topic-headings-in-notes

You can try out many of the commands in example/notes/org-mode-pubs.org.

Variables

Several variables determine where Bog looks for things.

• bog-bib-directory or bog-bib-file
• bog-file-directory
• bog-note-directory
• 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-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.

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.

Many of the Bog functions are useful outside of an Org buffer. You can turn Bog minor mode on (bog-mode) in non-Org buffers to get access to the keymap and citekey highlighting. To make Bog commands available from any buffer, bind bog-command-map to a global key.

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 nice 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 Org-ref.