bib2xml

NAME

bibutils - bibliography conversion utilities

SYNOPSIS

format2xml [ OPTIONS] [file.format]

xml2format [ OPTIONS] [file.xml]

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
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

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 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)

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

biblatex2xml 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

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

wordbib2xml convert a Word2007-formatted reference file to an XML-intermediate bibliogrpahy file.

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"
	      }

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.)

Chris Putnam, Ludwig Institute for Cancer Research[7]