    &dhemail;

2017 &dhusername; (Manual)
2008 Christopher Putnam (Software and Manual)

This manual page is distributed under the terms of version 2 of the GNU General Public License.

&dhdate;
&dhucpackage; &dhsection; &dhpackage; &version; User Commands
bibutils bibliography conversion utilities
`format2xml` OPTIONS file.format `xml2format` OPTIONS file.xml

## DESCRIPTION

The bibutils program set inter-converts between various bibliography formats using Library of Congress's Metadata Object Description Schema (MODS)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
- convert bibtex to MODS
- convert biblatex to MODS
- convert COPACformat references to MODS
- convert EBI XML to MODS
- convert EndNote (Refer format) to MODS
- convert EndNote XML to MODS
- 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
- convert RIS format to MODS
- 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) 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 . There are very nice instructions for making sure that you are properly exporting this at http://www.sonnysoftware.com/endnoteimport.html

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
- convert MODS into the SAO/NASA ADS format
- convert MODS into bibtex
- convert MODS into format for EndNote
- xml2isi convert MODS to ISI format
- convert MODS into RIS format
- 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) 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 (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 `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

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"}

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",}

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"}

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"
    }

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}
    	    }

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