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- _____
-
- BOG
- _____
-
-
-Table of Contents
-_________________
-
-1 Workflow
-2 Main features
-.. 2.1 Opening a PDF file for a citekey
-.. 2.2 Opening a BibTeX file for a citekey
-.. 2.3 Searching online for a citekey
-.. 2.4 Renaming new PDFs
-.. 2.5 Renaming new BibTeX files
-.. 2.6 Generating a combined BibTeX file
-3 Variables
-4 Recommended keybindings
-
-
-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.
-
-
-[Org mode] http://orgmode.org/
-
-
-1 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] [threads] 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:
- |
- | <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 nil
- | bibtex-autokey-titlewords-stretch 0
- | bibtex-autokey-titlewords 1
- | bibtex-autokey-year-title-separator "")
- `----
-
-
- [these] http://thread.gmane.org/gmane.emacs.orgmode/78983
-
- [threads] http://thread.gmane.org/gmane.emacs.orgmode/14756
-
-
-2 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.
-
-
-2.1 Opening a PDF file for a citekey
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- The function `bog-find-citekey-pdf' will open a PDF associated with a
- citekey.
-
-
-2.2 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 <citekey>.bib within a common directory
-
-
-2.3 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.
-
-
-2.4 Renaming new PDFs
-~~~~~~~~~~~~~~~~~~~~~
-
- New PDF files can be put in a "stage" directory and then renamed to a
- citekey.
-
-
-2.5 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.
-
-
-2.6 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.
-
-
-3 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.
-
-
-4 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)
- `----