1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
#+title: Bog
Bog is a system for taking research notes in [[http://orgmode.org/][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.
* 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 [[http://thread.gmane.org/gmane.emacs.orgmode/78983][these]] [[http://thread.gmane.org/gmane.emacs.orgmode/14756][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, but it shouldn't be so easy that I file them away
without giving them any thought. For me, this means glancing over it
at least enough to place it under a general topic (or capturing the
article and a link in my normal Org notes system until I take time to
refile it to my research notes). I only retrieve the BibTeX file or
PDF file when I need to use them.
* Features
** 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.
#+begin_example
# In a very general topic file
,* Topic heder
,** name2000word :atag:
<URL for study>
Article notes
#+end_example
"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.
#+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
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.
** Referencing studies within notes
You can reference other studies with their citekey.
#+begin_example
,** name2000word :atag:
Another study (another1999word).
#+end_example
"another1999word" will be highlighted within the text. When the point is
within the citekey, many Bog functions can extract and use the citekey.
** Opening a PDF file for a citekey
All PDF files are kept in a single directory and are named as
<citekey>-*.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.
** 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 [[Opening%20a%20PDF%20file][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 <citekey>.bib within a common directory
** 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.
** 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%20a%20PDF%20file][Opening a PDF file]].)
** 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.
** 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.
* 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.
#+begin_src emacs-lisp
(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)
#+end_src
|