The bibutils program set interconverts between various bibliography formats using a common MODS-format XML intermediate. For example, one can convert RIS-format files to Bibtex by doing two transformations: RIS->MODS->Bibtex. By using a common intermediate for N formats, only 2N programs are required and not N²-N. These programs operate on the command line and are styled after standard UNIX-like filters.

I primarily use these tools at the command line, but they are suitable for scripting and have been incorporated into a number of different bibliographic projects.

The XML intermediate is the Library of Congress's Metadata Object Description Schema (MODS) version 3.1. This is a very flexible standard that should prove quite useful as the number of tools that directly interact with it increase. For other programmers working on tools for working with MODS, I've written a quick introduction.

Several flags available for the end2xml, endx2xml, bib2xml, ris2xml, med2xml, and copac2xml programs:

-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

-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 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 in.

bib2xml BibTeX_file.bib > output_file.xml

copac2xml converts a COPAC formatted reference file to a MODS XML-intermediate bibliography file.

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:

%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

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

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 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 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

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

Starting with 3.24, xml2bib output uses lowercase tags and mixed case reference types for better interaction with Emacs. The older behavior with all uppercase tags/reference types can still be generated using the command-line switch -U/--uppercase.

Command line options:

• -v, --version ; report version information
• -h, --help ; report help
• -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
• -s, --single-refperfile ; put one reference per file name by the reference number
• -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
• -U, --uppercase ; use all uppercase for tags (field names) and reference types (pre-3.24 behavior)
• -sk, --strictkey ; ensure only alphanumeric characters are used in BibTeX reference keys

@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"}

@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",}

@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"}

@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"
}

@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}
}

@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"
}

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

Command line options:

• -v, --version ; report version information
• -h, --help ; report help
• -s, --single-refperfile put one reference per file name by the reference number
• -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
  
  

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

Command line options:

• -v, --version ; report version information
• -h, --help ; report help
• -s, --single-refperfile put one reference per file name by the reference number
• -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
  
  

xml2wordbib converts the MODS XML bibliography to Word 2007-formatted XML bibliography file. xml2word usage is as for other tools

xml2wordbib xml_file.xml > output_file.word.xml

Command line options:

• -v, --version ; report version information
• -h, --help ; report help
• -s, --single-refperfile put one reference per file name by the reference number
• -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
  
  

How do I download the files?

Files can be saved by right-clicking on the link. This will pull up a context-sensitive menu, from which you should choose "Save Link As..." (or whatever the appropriate item is for your web browser). Simply clicking on the links frequently loads the binary into the browser window. Not terribly useful.

Downloads on this page are going to be archives of all of the executables (as zipped or tarred/gzipped files depending on the architecture).

The programs don't run for me. What am I doing wrong?

If you send me this question, I would immediately have to ask for more information. The follow items address specific problems.

• "command not found" The message "command not found" on Linux/UNIX/MacOSX systems indicates that the commands cannot be found. This could mean that the programs are not flagged as being executable (run "chmod ugo+x xml2bib" for the appropriate binaries) or the executables are not in your current path (and have to be specified directly like ./xml2bib). A quick web search on chmod or path variables should provide many detailed resources.
  
  
• I'm running MacOSX and I just get a terminal when I double-click on the programs. Simply put, this is not the way to run the programs. You want to run the terminal first and then issue the commands at the command line. It should be under Applications->Utilities->Terminal on most MacOSX systems I've seen. If you just double-click the program, the terminal corresponds to the input to the tool. Not so useful.
  
  Some links to get you started running the terminal in a standard UNIX-like fashion are at TerminalBasics.pdf [homepage.mac.com], [macdevcenter.com], and [ee.surrey.ac.uk].
  
  I'm happy to help with specific questions, but the more knowledgable you are the easier it will be to help (and I frankly don't have the time to help everyone learn basic UNIX).
  
  

I am very interested in bug reports and problems in conversions. Feel free to e-mail me if you run into these issues. The absolute best bug reports provide error messages from the operating systems and/or input and outputs that detail the problems. Please remember that I'm not looking over your shoulder and I cannot read your mind to figure out what you are doing--"It doesn't work." isn't a bug report I can help you with.

You have a MacOSX version, can you give me a MacOS9 version?

Sorry. I'd like to, but these programs assume a command-line interface with normal standard in, standard out, and stardard error along with command-line arguments. MacOSX is a fundamental change in the operating sysem with a BSD (UNIX-like) core that I'm taking advantage of to provide a MacOSX binary. On the other hand, I don't know that much about MacOS9, and if it is possible to generate a useful binary from these sources let me know.

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.)