/
00README
199 lines (146 loc) · 7.37 KB
/
00README
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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
BibTeX databases maintained in the lab:
master.bib - most of the database.
books.bib - most books are separated out here.
lab.bib - the lab's own publications are here.
Possibly useful scripts:
pubmed2bib - converts NCBI pubmed abstract to most of a new bibtex entry.
bibmerge - merges two bibtex databases
bibfmt - converts a bibtex entry to HTML
lookup - finds entries in bibtex database that match a keyword
bibdistill - extracts a .bib bibliography appropriate for one manuscript.
________________________________________________________________
1. How the database and the lab's article and book collections work (or,
rather, are supposed to work, and in many cases actually do):
The lab has a growing collection of articles on file. Feel free to
borrow articles from the file, so long as you return them. They are
indexed by "main" author. For authors with a lot of papers on file,
there will be a separate file for them (look for "Zuker, Michael").
If there's not a separate file, look in the generic file by first
letter of their name (Joe Sixpack would be in "S"). Many (most?) of
these articles are indexed in the lab's bibtex database.
Each paper article is marked in two ways. First, it has its bibtex
database key written on it (i.e. MathewsTurner99); and if that's
underlined, that means it's not just been assigned a key, it's
actually been entered in the database. Second, the name that we filed
the article under is (usually) circled.
(If you find articles where this is not true, fix it. If you find
articles we've filed that are not in the database yet, enter them, if
you have time.)
You can look up articles by keyword. For example:
% lookup Mathews
returns, among other things, the entry:
@Article{MathewsTurner99,
author = {D. H. Mathews and J. Sabina and M. Zuker and D. H. Turner},
title = {Expanded Sequence Dependence of Thermodynamic
Parameters Improves Prediction of {RNA} Secondary
Structure},
journal = JMB,
year = 1999,
volume = 288,
pages = {911--940},
filed = {Mathews},
pmid = 10329189,
}
The {filed} field tells you what name we indexed the article under, so
you can find it in our files. Not many of our .bib entries have this,
though, so usually you'll have to guess.
The PMID field is the pubmed identifier. This lets us use the .bib
database to automatically construct HTML links (see the bibfmt
script).
The books.bib database is specialized to books (duh). It should carry
unique isbn numbers for each book. But stupidly, it's currently put
this info in an unstructured note; this will change to an {isbn}
field. The reason is the same as for having a {pmid} field in the
articles: scripts can use the database to automatically construct
appropriate HTML links.
The lab.bib database is specialized to our own lab's publications. It
includes a {url} field, which links to the site of the online
publication, if any. Eventually it'll also include a field for the
link to our preprint server.
________________________________________________________________
2. Using the bibtex databases, especially when writing papers:
First get them from the CVS repository. They're in the lab's
repository, "selab", so make sure you set your CVSROOT appropriately;
either manually, or by an alias you set up in your .cshrc:
% setenv CVSROOT :ext:<yourusername>@skynet.wustl.edu:/repository/selab
% cvs checkout labbib
You now have a directory called "labbib/". Make sure your BibTeX
include path includes this directory. For instance, if you put
labbib in your home directory, and you also have your own bibtex
databases in lib/bib:
% setenv BIBINPUTS :$HOME/labbib:$HOME/lib/bib
In your .tex file, the \bibliography command to load the databases is:
\bibliography{master,books,lab}
The order is important: master needs to come first, because it contains
macro definitions (journal name abbreviations) that the other database
files use.
Remember that the bibtex database is under revision constantly.
To update your version from the CVS repository, (remember to have
$CVSROOT set right), and do:
% cvs update
________________________________________________________________
3. Adding to, or editing the bibtex database:
You can use the database without fear; when you venture to become bold
enough to add to it yourself, here's how to do it. CVS gives us the
ability to roll back any changes easily, so even if you screw up, the
worse that happens is we fix it. You can't lose any data.
Simplest way is to edit the .bib files directly.
Emacs has a convenient bibtex mode; for instance, in bibtex mode, C-c
C-e C-a starts a new article entry. "M-x describe-mode" to see the
documentation. My bibtex mode is customized a little in my .emacs
file; feel free to look at that.
If you add a new entry, you have to choose a unique key. Keys are
constructed from the first author's last name plus a two-digit
year. If that's not a unique enough name or if you want the key to be
retrievable on the senior authors' name too, from the senior author's
last name too. If the key still isn't unique, we add "b", "c", etc.
to the end. For example, Eddy94, MathewsTurner99, RivasEddy00,
RivasEddy00b, RivasEddy00c are typical keys. Write the key on the
paper article, so someone who gets the article knows it's been
indexed.
After editing, remember to commit your changes to CVS:
% cvs commit
You might feel safer creating a new file of your own, and merging it
into the master database later. I often do this. Say you've made your
own database, new.bib. To merge it into master.bib, use the "bibmerge"
command:
% bibmerge new.bib master.bib
If it complains about anything, fix what it's complaining about. If
not, it worked. master.bib now contains the merged databases.
master.bib.bck is a backup of the original master.bib; you can delete
that, if everything went well. You can delete new.bib too. Remember to
check in your updated master.bib:
% cvs commit
________________________________________________________________
4. Using pubmed2bib
From the NCBI PubMed abstract page, mouse-copy everything from the
journal line (starting at the first character of the journal name) to
after the PMID line, and paste that into:
% cat | pubmed2bib
hit return, and at the end of the resulting spew will be a skeleton
.bib entry. For example, from the abstract in:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14499004&dopt=Abstract
if we cut from
BMC Bioinformatics. 2003...
to
PMID: 14499004 [PubMed - as supplied by publisher]
and paste, we get:
@Article{,
author = {R. J. Klein and S. R. Eddy},
title = {{RSEARCH:} Finding Homologs of Single Structured {RNA} Sequences},
journal = {BMC Bioinformatics.},
year = 2003,
volume = 4,
pages = {44},
OPTfiled = {},
OPTmynote = {},
OPTpmid = 14499004,
}
You still have to assign it a key, and fill in the {filed} field, and
you might have to clean it up (remove that period after the journal;
look out for capitalization issues in the title; change journal names
to our standard database abbrevs like NAR, JMB, if you like). After
all that, in emacs, C-c C-c finishes the entry up and deletes any
unused OPT (optional) fields you didn't fill in.
________________________________________________________________
CVS $Id$