_____ BOG _____ Table of Contents _________________ 1 Bog workflow 2 Features .. 2.1 Adding citekeys to notes .. 2.2 Referencing studies within notes .. 2.3 Opening a PDF file for a citekey .. 2.4 Opening a BibTeX file for a citekey .. 2.5 Searching online for a citekey .. 2.6 Renaming a new PDF .. 2.7 Renaming a new BibTeX file .. 2.8 Generating a combined BibTeX file 3 Recommended keybindings Bog is a system for taking research notes in [Org mode]. As any Org user knows, Org handles notetaking beautifully. Bog just 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 Bog 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 workflow for Bog is based on these preferences: 1. I don't want to store a lot of metadata with my notes. The citekey is the unique identifier that I use to link the notes with the BibTeX and PDF files. With just the citekey, I should be able to access this. If desired, more information can be added (such as bibliographic properties that can be generated with org-bibtex), but this is not required. One of the reasons for this is #2. 2. I want to have low friction for adding articles to the notes, but not mindless. There is an endless stream of research articles, so it should be easy to add them. On the other hand, it shouldn't be so easy that I file them away without giving them any thought. For me, this means capturing the article and a link in my normal Org notes system. At some point, I glance over it enough to decide what general topic it should be in and refile it into a research notes file. I prefer adding BibTeX and PDF files lazily. My only requirement is that I put it in a relevant heading and that I name it with a proper citekey. I make sure to add a link to the study online. I only retrieve the BibTeX file or PDF file when I need to use them. [these] http://thread.gmane.org/gmane.emacs.orgmode/78983 [threads] http://thread.gmane.org/gmane.emacs.orgmode/14756 2 Features ========== 2.1 Adding citekeys to notes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ As mentioned above, when citekeys are added, they should be filed under the appropriate topic. I organize my research notes into a few files with broad topics then have one level of headers representing topics to file studies under. ,---- | # In a very general topic file | | * Topic heder | | ** name2000word :atag: | | | | Article notes `---- "name2000word" is the study header. Bog expects the study citekey to be the title or property of a heading. 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 "") `---- If the study was added when checking journals online, I tend to add the URL right under the heading. However, I often add citekeys from the references of an article that I'm reading. In this case, I often store only the heading. 2.2 Referencing studies within notes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You can reference other studies with their citekey. ,---- | ** name2000word :atag: | | Another study (another1999word). `---- "another1999word" will be highlighted within the text. When the point is within the citekey, many Bog functions can extract and use the citekey. 2.3 Opening a PDF file for a citekey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ All PDF files are kept in a single directory and are named as -*.pdf. The function `bog-find-citekey-pdf' will open a PDF associated with a citekey. If the point is on a citekey, it will open that citekey. Otherwise, it will use the citekey from the first parent heading that is a study. 2.4 Opening a BibTeX file for a citekey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The function `bog-find-citekey-bib' will open the BibTeX entry associated with a citekey. The citekey is obtained in the same way as the PDF 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 2.5 Searching online for a citekey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The function `bog-search-citekey-on-web' will perform a search with the citekey information. By default, Google Scholar is searched. The default citekey format (first author's last name, year, and first non-trivial word) usually contains enough information to make this search successful. 2.6 Renaming a new PDF ~~~~~~~~~~~~~~~~~~~~~~ New PDF files can be put in a "stage" directory and then renamed to a citekey. (The citekey can be taken from the notes context, as described in Opening a PDF file.) 2.7 Renaming a new BibTeX file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If a separate BibTeX file is used for each citekey, `bog-rename-and-clean-new-bib-files' can be used to rename all new BibTeX files. `bibtex-clean-entry' is used to clean the entry and autogenerate the key. 2.8 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 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 b bog-find-citekey-bib 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 "b" 'bog-find-citekey-bib) | (define-key bog-map "w" 'bog-search-citekey-on-web) `----