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med2xml

Langue: en

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Version: February 10, 2008 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

NAME

bibutils - bibliography conversion utilities

SYNOPSIS

format2xml [OPTIONS] [file.format]
xml2format [OPTIONS] [file.xml]

DESCRIPTION

The bibutils program set interconverts between various bibliography formats using m[blue]Library of Congressm[][1]'s m[blue]Metadata Object Description Schema (MODS)m[][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
copac2xml convert m[blue]COPACm[][3]format references 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

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 m[blue]www.kostis.netm[][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
-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

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
 

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 m[blue]http://www.sonnysoftware.com/endnoteimport.htmlm[][5]

Usage for end2xml is the same as bib2xml.

 end2xml endnote_file.end > output_file.xml
 

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
 

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 m[blue]www.kostis.netm[][4]) unicode is now a character set option
-s --single-refperfile put one reference per file name by the reference number

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 m[blue]ADS reference formatm[][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.)

m[blue]Chris Putnam, Ludwig Institute for Cancer Researchm[][7]


Copyright © 2008 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.html
http://www.sonnysoftware.com/endnoteimport.html
6.
ADS reference format
http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html
7.
Chris Putnam, Ludwig Institute for Cancer Research
http://www.scripps.edu/~cdputnam/
ATROCITÉ

P : Pourquoi t'as acheté le CD de "Notre dame de Paris" ? T'aimes ça ?
M : Nan ! C'est une preuve pour les générations futures... Les révisionnistes ne pourront pas dire que ça n'a pas existé !