NAME
bibutils - bibliography conversion utilities
SYNOPSIS
format2xml [OPTIONS] [file.format]
xml2format [OPTIONS] [file.xml]
DESCRIPTION
The bibutils program set interconverts between various bibliography
formats using Library of Congress[1]'s Metadata Object Description
Schema (MODS)[2]version 3.1. For example, one can convert RIS-format
files to Bibtex by doing two transformations: RIS->MODS->Bibtex.
CONVERTING TO MODS
Overview
Command Description
bib2xml convert bibtex to MODS
copac2xml convert COPAC[3]format references 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
modsclean a MODS to MODS converter
ris2xml convert RIS format to MODS
Common Options Converting to MODS
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
-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
--verbose verbose output
--debug very verbose output (mostly for
debugging)
bib2xml
bib2xml 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
copac2xml
copac2xmlconverts a COPAC formatted reference file to a MODS
XML-intermediate bibliography file.
end2xml
end2xml 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
endx2xml
endx2xml 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.
isi2xml
isi2xml 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
ris2xml
ris2xml 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
CONVERTING FROM MODS
Overview
Command Description
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
Common Options Converting from MODS
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
xml2bib
xml2bib 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-specific Options:
-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
xml2ads
xml2ads converts the MODS XML bibliography to the Smithsonian
Astrophysical Observatory (SAO)/National Aeronautics and Space
Administration (NASA) Astrophyics Data System or ADS reference
format[6] (which is very similar to the tagged Endnote style). xml2ads
usage is as for other tools
xml2ads xml_file.xml > output_file.ads
xml2ris
xml2ris converts the MODS XML bibliography to RIS-formatted
bibliography file. xml2ris usage is as for other tools
xml2ris xml_file.xml > output_file.ris
xml2end
xml2end 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
xml2wordbib
xml2wordbib 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.
EXAMPLES
Example 1. Example refer format file
%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
xml2bib Output Variations
Example 2. 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"}
Example 3. Final Comma
@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",}
Example 4. Single Dash
@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"}
Example 5. 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"
}
Example 6. 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}
}
Example 7. 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 relased under the GNU 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.)
Chris Putnam, Ludwig Institute for Cancer Research[7]
COPYRIGHT
Copyright © 2008 David Bremner (Manual)
Copyright © 2008 Christopher Putnam (Software and Manual)
This manual page is distributed under the terms of version 2 of the GNU
General Public License.
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.html
http://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.scripps.edu/~cdputnam/