1BIBUTILS(1)                      User Commands                     BIBUTILS(1)
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3
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NAME

6       bibutils - bibliography conversion utilities
7

SYNOPSIS

9       format2xml [OPTIONS] [file.format]
10
11       xml2format [OPTIONS] [file.xml]
12

DESCRIPTION

14       The bibutils program set inter-converts between various bibliography
15       formats using Library of Congress[1]'s Metadata Object Description
16       Schema (MODS)[2]version 3.1. For example, one can convert RIS-format
17       files to Bibtex by doing two transformations: RIS->MODS->Bibtex.
18

CONVERTING TO MODS

20   Overview
21       Command        Description
22       bib2xml        convert bibtex to MODS
23       biblatex2xml   convert biblatex to MODS
24       copac2xml      convert COPAC[3]format references to MODS
25       ebi2xml        convert EBI XML to MODS
26       end2xml        convert EndNote (Refer format) to MODS
27       endx2xml       convert EndNote XML to MODS
28       isi2xml        convert ISI web of science to MODS
29       med2xml        convert Pubmed XML references to MODS
30       nbib2xml       convert Pubmed nbib format references to
31                      MODS
32       modsclean      a MODS to MODS converter
33       ris2xml        convert RIS format to MODS
34       wordbib2xml    convert Word2007 bibliography XML to MODS
35
36
37   Common Options Converting to MODS
38       Several flags available for the end2xml, endx2xml, bib2xml, ris2xml,
39       med2xml, and copac2xml programs. Most options have both a short and a
40       long version.
41
42
43       -h    --help                 display help
44       -v    --version              display version
45       -a    --add-refcount         add "_#", where # is reference
46                                    count to reference id
47       -s    --single-refperfile    put one reference per file name
48                                    by the reference number
49       -i    --input-encoding       interpret the input file as
50                                    using the requested character
51                                    set (use w/o argument for
52                                    current list derived from
53                                    character sets at
54                                    www.kostis.net[4]) unicode is
55                                    now a character set option
56       -u    --unicode-characters   encode unicode characters
57                                    directly in the file rather
58                                    than as XML entities
59       -un   --unicode-no-bom       as -u, but don't include a byte
60                                    order mark
61       -x    --xml-entities         encode unicode characters as
62                                    XML entities (opposite of -u)
63       -nl   --no-latex             do not convert latex-style
64                                    character combinations
65       -s    --single-refperfile    one reference per output file
66
67       -d    --drop-key             don't put citation key in the
68                                    mods id field
69       -c    --corporation-file     with argument specifying a file
70                                    containing a list of
71                                    corporation names to be placed
72                                    in <name
73                                    type="corporate"></name>
74                                    instead of type="personal" and
75                                    eliminate name mangling
76       -a    --asis                 with argument specifying a file
77                                    containing a list of names to
78                                    be treated verbatim
79       -nt   --nosplit-title        don't split titles into
80                                    TITLE/SUBTITLE pairs
81             --verbose              verbose output
82             --debug                very verbose output (mostly for
83                                    debugging)
84
85
86   bib2xml
87       bib2xml converts a bibtex-formatted reference file to an
88       XML-intermediate bibliography file. Specify file(s) to be converted on
89       the command line. Files containing bibtex substitutions strings should
90       be specified before the files where substitutions are specified (or in
91       the same file before their use). If no files are specified, then bibtex
92       information will be read from standard input.
93
94           bib2xml bibtex_file.bib > output_file.xml
95
96   biblatex2xml
97       biblatex2xml converts a biblatex (not to be confused with bibtex)
98       formatted reference file to an MODS XML-intermediate bibliography file.
99
100           biblatex2xml biblatex_file.bib > outputfile.xml
101
102   copac2xml
103       copac2xmlconverts a COPAC formatted reference file to a MODS
104       XML-intermediate bibliography file.
105
106   end2xml
107       end2xml converts a text endnote-formatted reference file to an
108       XML-intermediate bibliography file. This program will not work on the
109       binary library; the file needs to be exported first. Endnote tagged
110       formats ("Refer" format export) look like Example 1, “Example refer
111       format file”. There are very nice instructions for making sure that you
112       are properly exporting this at
113       http://www.sonnysoftware.com/endnoteimport.html[5]
114
115       Usage for end2xml is the same as bib2xml.
116
117           end2xml endnote_file.end > output_file.xml
118
119   ebi2xml
120       ebi2xml converts a EBI XML file to a MODS XML-intermediate bibliography
121       file.
122
123   endx2xml
124       endx2xml converts a EndNote-XML exported reference file to a MODS
125       XML-intermediate bibliography file. This program will not work on the
126       binary library; the file needs to be exported first.
127
128   isi2xml
129       isi2xml converts an ISI-web-of-science-formatted reference file to an
130       XML-intermediate bibliography file.
131
132       Usage for isi2xml is the same as bib2xml.
133
134           isi2xml input_file.isi > output_file.xml
135
136   ris2xml
137       ris2xml converts a RIS-formatted reference file to an XML-intermediate
138       bibliography file.  ris2xml usage is as end2xml and bib2xml
139
140           ris2xml ris_file.ris >output_file.xml
141
142   wordbib2xml
143       wordbib2xml convert a Word2007-formatted reference file to an
144       XML-intermediate bibliogrpahy file.
145

CONVERTING FROM MODS

147   Overview
148       Command       Description
149       xml2ads       convert MODS into the SAO/NASA ADS format
150       xml2bib       convert MODS into bibtex
151       xml2end       convert MODS into format for EndNote
152       xml2isi       convert MODS to ISI format
153       xml2ris       convert MODS into RIS format
154       xml2wordbib   convert MODS into Word 2007 bibliography
155                     format
156
157
158   Common Options Converting from MODS
159       Note that --output-encoding refers to the input file
160
161
162       -h    --help                display help
163       -v    --version             display version
164       -o    --output-encoding     interpret the input file as
165                                   using the requested character
166                                   set (use w/o argument for
167                                   current list derived from
168                                   character sets at
169                                   www.kostis.net[4]) unicode is
170                                   now a character set option
171       -s    --single-refperfile   put one reference per file name
172                                   by the reference number
173       -nb   --no-bom              do not write Byte Order Mark if
174                                   writing UTF8
175
176
177   xml2bib
178       xml2bib converts the MODS XML bibliography into a bibtex-formatted
179       reference file.  xml2bib usage is as for other tools
180
181           xml2bib xml_file.xml > output_file.bib
182
183       Since the BibTeX reference format is fairly flexible and seems to have
184       the greatest number of personal preferences, it has also accumulated a
185       number of specific options that are not available for other formats.
186
187       Starting with 3.24, xml2bib output uses lowercase tags and mixed case
188       reference types for better interaction with other software. The older
189       behavior with all uppercase tags/reference types can still be generated
190       using the command-line switch -U/--uppercase.
191
192       xml2bib-specific Options:
193
194           -fc   --finalcomma   add final comma in the bibtex
195                                output for those that want it
196
197
198
199           -sd   --singledash   use one dash instead of two
200                                (longer dash in latex) between
201                                numbers in page output
202           -b    --brackets     use brackets instead of
203                                quotation marks around field
204                                data
205           -w    --whitespace   add beautifying whitespace to
206                                output
207           -U    --uppercase    use all uppercase for tags
208                                (field names) and reference
209                                types (pre-3.24 behavior)
210           -sk   --strictkey    only use alphanumeric
211                                characters for bibtex citation
212                                keys
213
214
215   xml2ads
216       xml2ads converts the MODS XML bibliography to the Smithsonian
217       Astrophysical Observatory (SAO)/National Aeronautics and Space
218       Administration (NASA) Astrophyics Data System or ADS reference
219       format[6] (which is very similar to the tagged Endnote style).  xml2ads
220       usage is as for other tools
221
222           xml2ads xml_file.xml > output_file.ads
223
224   xml2ris
225       xml2ris converts the MODS XML bibliography to RIS-formatted
226       bibliography file.  xml2ris usage is as for other tools
227
228           xml2ris xml_file.xml > output_file.ris
229
230   xml2end
231       xml2end converts the MODS XML bibliography to tagged Endnote
232       (refer-format) bibliography file.  xml2end usage is as for other tools
233
234           xml2end xml_file.xml >  output_file.end
235
236   xml2wordbib
237       xml2wordbib converts the MODS XML bibliography to Word 2007-formatted
238       XML bibliography file.  xml2wordbib usage is as for other tools
239
240           xml2wordbib xml_file.xml >  output_file.word.xml
241
242       xml2wordbib was called xml2word in versions of bibutils prior to 3.40.
243       It was renamed to avoid confusion with other tools. Hopefully this will
244       not break too many scripts already in use.
245

EXAMPLES

247       Example 1. Example refer format file
248
249           %0 Journal Article
250           %A C. D. Putnam
251           %A C. S. Pikaard
252           %D 1992
253           %T Cooperative binding of the Xenopus RNA polymerase I
254              transcription factor xUBF to repetitive ribosomal gene enhancers
255           %J Mol Cell Biol
256           %V 12
257           %P 4970-4980
258           %F Putnam1992
259
260   xml2bib Output Variations
261       Example 2. Default
262
263                 @Article{Putnam1992,
264                 author="C. D. Putnam
265                 and C. S. Pikaard",
266                 year="1992",
267                 month="Nov",
268                 title="Cooperative binding of the
269                 Xenopus RNA polymerase I transcription
270                 factor xUBF to repetitive ribosomal
271                 gene enhancers",
272                 journal="Mol Cell Biol",
273                 volume="12",
274                 pages="4970--4980",
275                 number="11"}
276
277
278       Example 3. Final Comma
279
280                 @Article{Putnam1992,
281                 author="C. D. Putnam
282                 and C. S. Pikaard",
283                 year="1992",
284                 month="Nov",
285                 title="Cooperative binding of the
286                 Xenopus RNA polymerase I transcription
287                 factor xUBF to repetitive ribosomal
288                 gene enhancers",
289                 journal="Mol Cell Biol",
290                 volume="12",
291                 pages="4970--4980",
292                 number="11",}
293
294
295       Example 4. Single Dash
296
297                 @Article{Putnam1992,
298                 author="C. D. Putnam
299                 and C. S. Pikaard",
300                 year="1992",
301                 month="Nov",
302                 title="Cooperative binding of the
303                 Xenopus RNA polymerase I transcription
304                 factor xUBF to repetitive ribosomal
305                 gene enhancers",
306                 journal="Mol Cell Biol",
307                 volume="12",
308                 pages="4970-4980",
309                 number="11"}
310
311
312       Example 5. Whitespace
313
314           @Article{Putnam1992,
315             author =      "C. D. Putnam
316                           and C. S. Pikaard",
317             year =        "1992",
318             month =       "Jan",
319             title =       "Cooperative binding of
320           the Xenopus RNA polymerase I transcription
321           factor xUBF to repetitive ribosomal gene
322           enhancers",
323             journal =     "Mol Cell Biol",
324             volume =      "12",
325             pages =       "4970--4980"
326           }
327
328       Example 6. Brackets
329
330               @Article{Putnam1992,
331               author={Putnam, C. D.
332               and Pikaard, C. S.},
333               title={Cooperative binding of the Xenopus
334               RNA polymerase I transcription factor xUBF
335               to repetitive ribosomal gene enhancers},
336               journal={Mol Cell Biol},
337               year={1992},
338               month={Nov},
339               volume={12},
340               number={11},
341               pages={4970--4980}
342               }
343
344
345       Example 7. Uppercase
346
347                 @ARTICLE{Putnam1992,
348                 AUTHOR="Putnam, C. D.
349                 and Pikaard, C. S.",
350                 TITLE="Cooperative binding of the Xenopus
351                 RNA polymerase I transcription factor xUBF
352                 to repetitive ribosomal gene enhancers",
353                 JOURNAL="Mol Cell Biol",
354                 YEAR="1992",
355                 MONTH="Nov",
356                 VOLUME="12",
357                 NUMBER="11",
358                 PAGES="4970--4980"
359                 }
360
361

LICENSE

363       All versions of bibutils are relased under the GNU Public License
364       (GPL). In a nutshell, feel free to download, run, and modify these
365       programs as required. If you re-release these, you need to release the
366       modified version of the source. (And I'd appreciate patches as
367       well...if you care enough to make the change, then I'd like to see what
368       you're adding or fixing.)
369
370       Chris Putnam, Ludwig Institute for Cancer Research[7]
371
373       Copyright © 2017 David Bremner (Manual)
374       Copyright © 2008 Christopher Putnam (Software and Manual)
375
376       This manual page is distributed under the terms of version 2 of the GNU
377       General Public License.
378
379

NOTES

381        1. Library of Congress
382           http://www.loc.gov
383
384        2. Metadata Object Description Schema (MODS)
385           http://www.loc.gov/standards/mods/
386
387        3. COPAC
388           http://copac.ac.uk/
389
390        4. www.kostis.net
391           http://www.kostis.net/
392
393        5. http://www.sonnysoftware.com/endnoteimport.html
394           http://www.sonnysoftware.com/endnoteimport.html
395
396        6. ADS reference format
397           http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html
398
399        7. Chris Putnam, Ludwig Institute for Cancer Research
400           http://www.sourceforge.net/p/bibutils/home/Bibutils
401
402
403
404bibutils 6.10                  November 8, 2016                    BIBUTILS(1)
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