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bibutils - bibliography conversion utilities
Contents
Converting From Mods
OverviewCommandDescription
xml2ads convert MODS into the SAO/NASA ADS format
xml2bib convert MODS into bibtex
xml2end convert MODS into format for EndNote
xml2isi convert MODS to ISI format
xml2ris convert MODS into RIS format
xml2wordbib convert MODS into Word 2007 bibliography format
CommonOptionsConvertingfromMODS
Note that --output-encoding refers to the input file
-h --help display help
-v --version display version
-o --output-encoding interpret the input file as using the
requested character set (use w/o argument for
current list derived from character sets at
www.kostis.net[4]) unicode is now a character
set option
-s --single-refperfile put one reference per file name by the
reference number
-nb --no-bom do not write Byte Order Mark if writing UTF8
xml2bibxml2bib converts the MODS XML bibliography into a bibtex-formatted reference file. xml2bib usage is as
for other tools
xml2bib xml_file.xml > output_file.bib
Since the BibTeX reference format is fairly flexible and seems to have the greatest number of personal
preferences, it has also accumulated a number of specific options that are not available for other
formats.
Starting with 3.24, xml2bib output uses lowercase tags and mixed case reference types for better
interaction with other software. The older behavior with all uppercase tags/reference types can still be
generated using the command-line switch -U/--uppercase.
xml2bib-specificOptions:
-fc --finalcomma add final comma in the bibtex output for
those that want it
-sd --singledash use one dash instead of two (longer dash in
latex) between numbers in page output
-b --brackets use brackets instead of quotation marks
around field data
-w --whitespace add beautifying whitespace to output
-U --uppercase use all uppercase for tags (field names) and
reference types (pre-3.24 behavior)
-sk --strictkey only use alphanumeric characters for bibtex
citation keys
xml2adsxml2ads converts the MODS XML bibliography to the Smithsonian Astrophysical Observatory (SAO)/National
Aeronautics and Space Administration (NASA) Astrophyics Data System or ADSreferenceformat[6] (which is
very similar to the tagged Endnote style). xml2ads usage is as for other tools
xml2ads xml_file.xml > output_file.ads
xml2risxml2ris converts the MODS XML bibliography to RIS-formatted bibliography file. xml2ris usage is as for
other tools
xml2ris xml_file.xml > output_file.ris
xml2endxml2end converts the MODS XML bibliography to tagged Endnote (refer-format) bibliography file. xml2end
usage is as for other tools
xml2end xml_file.xml > output_file.end
xml2wordbibxml2wordbib converts the MODS XML bibliography to Word 2007-formatted XML bibliography file. xml2wordbib
usage is as for other tools
xml2wordbib xml_file.xml > output_file.word.xml
xml2wordbib was called xml2word in versions of bibutils prior to 3.40. It was renamed to avoid confusion
with other tools. Hopefully this will not break too many scripts already in use.
Converting To Mods
OverviewCommandDescription
bib2xml convert bibtex to MODS
biblatex2xml convert biblatex to MODS
copac2xml convert COPAC[3]format references to MODS
ebi2xml convert EBI XML to MODS
end2xml convert EndNote (Refer format) to MODS
endx2xml convert EndNote XML to MODS
isi2xml convert ISI web of science to MODS
med2xml convert Pubmed XML references to MODS
nbib2xml convert Pubmed nbib format references to MODS
modsclean a MODS to MODS converter
ris2xml convert RIS format to MODS
wordbib2xml convert Word2007 bibliography XML to MODS
CommonOptionsConvertingtoMODS
Several flags available for the end2xml, endx2xml, bib2xml, ris2xml, med2xml, and copac2xml programs.
Most options have both a short and a long version.
-h --help display help
-v --version display version
-a --add-refcount add "_#", where # is reference count to
reference id
-s --single-refperfile put one reference per file name by the
reference number
-i --input-encoding interpret the input file as using the
requested character set (use w/o argument for
current list derived from character sets at
www.kostis.net[4]) unicode is now a character
set option
-u --unicode-characters encode unicode characters directly in the
file rather than as XML entities
-un --unicode-no-bom as -u, but don't include a byte order mark
-x --xml-entities encode unicode characters as XML entities
(opposite of -u)
-nl --no-latex do not convert latex-style character
combinations
-s --single-refperfile one reference per output file
-d --drop-key don't put citation key in the mods id field
-c --corporation-file with argument specifying a file containing a
list of corporation names to be placed in
<name type="corporate"></name> instead of
type="personal" and eliminate name mangling
-a --asis with argument specifying a file containing a
list of names to be treated verbatim
-nt --nosplit-title don't split titles into TITLE/SUBTITLE pairs
--verbose verbose output
--debug very verbose output (mostly for debugging)
bib2xmlbib2xml converts a bibtex-formatted reference file to an XML-intermediate bibliography file. Specify
file(s) to be converted on the command line. Files containing bibtex substitutions strings should be
specified before the files where substitutions are specified (or in the same file before their use). If
no files are specified, then bibtex information will be read from standard input.
bib2xml bibtex_file.bib > output_file.xml
biblatex2xmlbiblatex2xml converts a biblatex (not to be confused with bibtex) formatted reference file to an MODS
XML-intermediate bibliography file.
biblatex2xml biblatex_file.bib > outputfile.xml
copac2xmlcopac2xmlconverts a COPAC formatted reference file to a MODS XML-intermediate bibliography file.
end2xmlend2xml converts a text endnote-formatted reference file to an XML-intermediate bibliography file. This
program will not work on the binary library; the file needs to be exported first. Endnote tagged formats
("Refer" format export) look like Example 1, “Example refer format file”. There are very nice
instructions for making sure that you are properly exporting this at
http://www.sonnysoftware.com/endnoteimport.html[5]
Usage for end2xml is the same as bib2xml.
end2xml endnote_file.end > output_file.xml
ebi2xmlebi2xml converts a EBI XML file to a MODS XML-intermediate bibliography file.
endx2xmlendx2xml converts a EndNote-XML exported reference file to a MODS XML-intermediate bibliography file.
This program will not work on the binary library; the file needs to be exported first.
isi2xmlisi2xml converts an ISI-web-of-science-formatted reference file to an XML-intermediate bibliography file.
Usage for isi2xml is the same as bib2xml.
isi2xml input_file.isi > output_file.xml
ris2xmlris2xml converts a RIS-formatted reference file to an XML-intermediate bibliography file. ris2xml usage
is as end2xml and bib2xml
ris2xml ris_file.ris > output_file.xml
wordbib2xmlwordbib2xml convert a Word2007-formatted reference file to an XML-intermediate bibliogrpahy file.
Copyright
Copyright © 2021 David Bremner (Manual)
Copyright © 2021 Christopher Putnam (Software and Manual)
This manual page is distributed under the terms of version 2 of the GNU General Public License.
Description
The bibutils program set inter-converts between various bibliography formats using LibraryofCongress[1]'s MetadataObjectDescriptionSchema(MODS)[2]version 3.1. For example, one can convert
RIS-format files to Bibtex by doing two transformations: RIS->MODS->Bibtex.
Examples
Example1.Examplereferformatfile
%0 Journal Article
%A C. D. Putnam
%A C. S. Pikaard
%D 1992
%T Cooperative binding of the Xenopus RNA polymerase I
transcription factor xUBF to repetitive ribosomal gene enhancers
%J Mol Cell Biol
%V 12
%P 4970-4980
%F Putnam1992
xml2bibOutputVariationsExample2.Default
@Article{Putnam1992,
author="C. D. Putnam
and C. S. Pikaard",
year="1992",
month="Nov",
title="Cooperative binding of the
Xenopus RNA polymerase I transcription
factor xUBF to repetitive ribosomal
gene enhancers",
journal="Mol Cell Biol",
volume="12",
pages="4970--4980",
number="11"}
Example3.FinalComma
@Article{Putnam1992,
author="C. D. Putnam
and C. S. Pikaard",
year="1992",
month="Nov",
title="Cooperative binding of the
Xenopus RNA polymerase I transcription
factor xUBF to repetitive ribosomal
gene enhancers",
journal="Mol Cell Biol",
volume="12",
pages="4970--4980",
number="11",}
Example4.SingleDash
@Article{Putnam1992,
author="C. D. Putnam
and C. S. Pikaard",
year="1992",
month="Nov",
title="Cooperative binding of the
Xenopus RNA polymerase I transcription
factor xUBF to repetitive ribosomal
gene enhancers",
journal="Mol Cell Biol",
volume="12",
pages="4970-4980",
number="11"}
Example5.Whitespace
@Article{Putnam1992,
author = "C. D. Putnam
and C. S. Pikaard",
year = "1992",
month = "Jan",
title = "Cooperative binding of
the Xenopus RNA polymerase I transcription
factor xUBF to repetitive ribosomal gene
enhancers",
journal = "Mol Cell Biol",
volume = "12",
pages = "4970--4980"
}
Example6.Brackets
@Article{Putnam1992,
author={Putnam, C. D.
and Pikaard, C. S.},
title={Cooperative binding of the Xenopus
RNA polymerase I transcription factor xUBF
to repetitive ribosomal gene enhancers},
journal={Mol Cell Biol},
year={1992},
month={Nov},
volume={12},
number={11},
pages={4970--4980}
}
Example7.Uppercase
@ARTICLE{Putnam1992,
AUTHOR="Putnam, C. D.
and Pikaard, C. S.",
TITLE="Cooperative binding of the Xenopus
RNA polymerase I transcription factor xUBF
to repetitive ribosomal gene enhancers",
JOURNAL="Mol Cell Biol",
YEAR="1992",
MONTH="Nov",
VOLUME="12",
NUMBER="11",
PAGES="4970--4980"
}
License
All versions of bibutils are released under the GNU General Public License (GPL). In a nutshell, feel
free to download, run, and modify these programs as required. If you re-release these, you need to
release the modified version of the source. (And I'd appreciate patches as well...if you care enough to
make the change, then I'd like to see what you're adding or fixing.)
ChrisPutnam,LudwigInstituteforCancerResearch[7]
Name
bibutils - bibliography conversion utilities
Notes
1. Library of Congress
http://www.loc.gov
2. Metadata Object Description Schema (MODS)
http://www.loc.gov/standards/mods/
3. COPAC
http://copac.ac.uk/
4. www.kostis.net
http://www.kostis.net/
5. http://www.sonnysoftware.com/endnoteimport.htmlhttp://www.sonnysoftware.com/endnoteimport.html
6. ADS reference format
http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html
7. Chris Putnam, Ludwig Institute for Cancer Research
http://www.sourceforge.net/p/bibutils/home/Bibutils
bibutils 7.2 November 8, 2016 BIBUTILS(1)
Synopsis
format2xml [OPTIONS] [file.format]
xml2format [OPTIONS] [file.xml]
PNG Icons
