Table of Contents

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. # 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 [these](http://thread.gmane.org/gmane.emacs.orgmode/78983) [threads](http://thread.gmane.org/gmane.emacs.orgmode/14756) 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 and PDF 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). * 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 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. If one isn't found, the user will be prompted for the citekey. ## Opening a PDF file for a citekey The function `bog-find-citekey-pdf` will open a PDF associated with a citekey. ## Opening a BibTeX file for a citekey The function `bog-find-citekey-bib` will open the BibTeX entry associated with a 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 .bib within a common directory ## Searching online for a citekey The function `bog-search-citekey-on-web` will perform a Google Scholar search with the citekey information. 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 new PDFs New PDF files can be put in a "stage" directory and then renamed to a citekey. ## Renaming new BibTeX files If a separate BibTeX file is used for each citekey, `bog-clean-and-rename-staged-bibs` 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. # Variables Several variables determine where Bog looks for things. - bog-notes-directory - bog-pdf-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-func:** 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-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. # 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 r bog-rename-staged-pdf-to-citekey
C-c b b bog-find-citekey-bib
C-c b h bog-goto-citekey-heading-in-buffer
C-c b H bog-goto-citekey-heading-in-notes
C-c b w bog-search-citekey-on-web
This can be achieved by placing the code below in your .emacs file. (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 "r" 'bog-rename-staged-pdf-to-citekey) (define-key bog-map "b" 'bog-find-citekey-bib) (define-key bog-map "h" 'bog-goto-citekey-heading-in-buffer) (define-key bog-map "H" 'bog-goto-citekey-heading-in-notes) (define-key bog-map "w" 'bog-search-citekey-on-web)