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bibutils

man page of bibutils

bibutils: bibliography conversion utilities

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 //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 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 (C) 2010 David Bremner (Manual) Copyright (C) 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 //www.loc.gov 2. Metadata Object Description Schema (MODS) //www.loc.gov/standards/mods/ 3. COPAC //copac.ac.uk/ 4. www.kostis.net //www.kostis.net/ 5. //www.sonnysoftware.com/endnoteimport.html //www.sonnysoftware.com/endnoteimport.html 6. ADS reference format //doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html 7. Chris Putnam, Ludwig Institute for Cancer Research //www.scripps.edu/~cdputnam/ BIBUTILS(1)
 
 
 

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