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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.php[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"
                 }

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 © 2010 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.php
           http://www.sonnysoftware.com/endnoteimport.php

        6. ADS reference format
           http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.php

        7. Chris Putnam, Ludwig Institute for Cancer Research
           http://www.scripps.edu/~cdputnam/



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