1BIBUTILS(1) User Commands BIBUTILS(1)
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6 bibutils - bibliography conversion utilities
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9 format2xml [OPTIONS] [file.format]
10 xml2format [OPTIONS] [file.xml]
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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
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 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 -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 -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 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 bib2xml bibtex_file.bib > output_file.xml
95 biblatex2xml
97 biblatex2xml converts a biblatex (not to be confused with bibtex)
98 formatted reference file to an MODS XML-intermediate bibliography file.
99 biblatex2xml biblatex_file.bib > outputfile.xml
101 copac2xml
103 copac2xmlconverts a COPAC formatted reference file to a MODS
104 XML-intermediate bibliography file.
105 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 Usage for end2xml is the same as bib2xml.
116 end2xml endnote_file.end > output_file.xml
118 ebi2xml
120 ebi2xml converts a EBI XML file to a MODS XML-intermediate bibliography
121 file.
122 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 isi2xml
129 isi2xml converts an ISI-web-of-science-formatted reference file to an
130 XML-intermediate bibliography file.
131 Usage for isi2xml is the same as bib2xml.
133 isi2xml input_file.isi > output_file.xml
135 ris2xml
137 ris2xml converts a RIS-formatted reference file to an XML-intermediate
138 bibliography file. ris2xml usage is as end2xml and bib2xml
139 ris2xml ris_file.ris >output_file.xml
141 wordbib2xml
143 wordbib2xml convert a Word2007-formatted reference file to an
144 XML-intermediate bibliogrpahy file.
145
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 Common Options Converting from MODS
159 Note that --output-encoding refers to the input file
160 -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 xml2bib
178 xml2bib converts the MODS XML bibliography into a bibtex-formatted
179 reference file. xml2bib usage is as for other tools
180 xml2bib xml_file.xml > output_file.bib
182 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 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 xml2bib-specific Options:
193 -fc --finalcomma add final comma in the bibtex
195 output for those that want it
196 -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 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 xml2ads xml_file.xml > output_file.ads
223 xml2ris
225 xml2ris converts the MODS XML bibliography to RIS-formatted
226 bibliography file. xml2ris usage is as for other tools
227 xml2ris xml_file.xml > output_file.ris
229 xml2end
231 xml2end converts the MODS XML bibliography to tagged Endnote
232 (refer-format) bibliography file. xml2end usage is as for other tools
233 xml2end xml_file.xml > output_file.end
235 xml2wordbib
237 xml2wordbib converts the MODS XML bibliography to Word 2007-formatted
238 XML bibliography file. xml2wordbib usage is as for other tools
239 xml2wordbib xml_file.xml > output_file.word.xml
241 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
247 Example 1. Example refer format file
248 %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 xml2bib Output Variations
261 Example 2. Default
262 @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 Example 3. Final Comma
279 @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 Example 4. Single Dash
296 @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 Example 5. Whitespace
313 @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 Example 6. Brackets
329 @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 Example 7. Uppercase
346 @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
363 All versions of bibutils are released under the GNU General Public
364 License (GPL). In a nutshell, feel free to download, run, and modify
365 these programs as required. If you re-release these, you need to
366 release the modified version of the source. (And I'd appreciate patches
367 as well...if you care enough to make the change, then I'd like to see
368 what you're adding or fixing.)
369 Chris Putnam, Ludwig Institute for Cancer Research[7]
371
373 Copyright © 2021 David Bremner (Manual)
374 Copyright © 2021 Christopher Putnam (Software and Manual)
375 This manual page is distributed under the terms of version 2 of the GNU
377 General Public License.
378
381 1. Library of Congress
382 http://www.loc.gov
383 2. Metadata Object Description Schema (MODS)
385 http://www.loc.gov/standards/mods/
386 3. COPAC
388 http://copac.ac.uk/
389 4. www.kostis.net
391 http://www.kostis.net/
392 5. http://www.sonnysoftware.com/endnoteimport.html
394 http://www.sonnysoftware.com/endnoteimport.html
395 6. ADS reference format
397 http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html
398 7. Chris Putnam, Ludwig Institute for Cancer Research
400 http://www.sourceforge.net/p/bibutils/home/Bibutils
401bibutils 7.2 November 8, 2016 BIBUTILS(1)