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@@ -1,148 +0,0 @@ -# -*- mode: org -*- -#+title: Bog -#+options: toc:nil -#+startup: showall - -Bog is a system for taking research notes in [[http://orgmode.org/][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 [[http://melpa.milkbox.net/][MELPA]]. - -To enable Bog in all Org buffers, add it to =org-mode-hook=. - -#+begin_src emacs-lisp - (add-hook 'org-mode-hook 'bog-mode) -#+end_src - -* 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). - -#+begin_example - - ,* Topic heading - - ,** TODO name2000word :atag: - - <URL for study> - - Article notes ... a reference to another1999study ... -#+end_example - -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 - -* 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-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= -- =bog-open-first-citekey-link= - -* 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 [[http://thread.gmane.org/gmane.emacs.orgmode/78983][nice]] -[[http://thread.gmane.org/gmane.emacs.orgmode/14756][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 [[https://github.com/jkitchin/jmax/blob/master/org/org-ref.org][Org-ref]]. |