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PROGRAM:

NAME

bibutils - bibliography conversion utilities

SYNOPSIS

format2xml [OPTIONS] [file.format]

xml2format [OPTIONS] [file.xml]

DESCRIPTION

The bibutils program set inter-converts 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
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
modsclean a MODS to MODS converter
ris2xml convert RIS format to MODS
wordbib2xml convert Word2007 bibliography XML 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
-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 be treated
verbatim
-nt --nosplit-title don't split titles into TITLE/SUBTITLE
pairs
--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

biblatex2xml
bib2xml converts a biblatex (not to be confused with bibtex) formatted reference file to
an XML-intermediate bibliography file. .

bib2xml biblatex_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

ebi2xml
ebi2xml converts a EBI XML file to a MODS XML-intermediate bibliography file.

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

wordbib2xml
ris2xml converts a RIS-formatted reference file to an XML-intermediate bibliography file.
ris2xml usage is as end2xml and bib2xml

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
-nb --no-bom do not write Byte Order Mark if writing
UTF8

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"
}

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