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 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: 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` - `bog-insert-heading-citekey` # 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 [nice](http://thread.gmane.org/gmane.emacs.orgmode/78983) [descriptions](http://thread.gmane.org/gmane.emacs.orgmode/14756) 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](https://github.com/jkitchin/jmax/blob/master/org/org-ref.org).