Bibutils - Revision history

WikiSysop: Group list of Bibutils conversions

2023-11-05T20:16:15Z

Group list of Bibutils conversions

← Older revision		Revision as of 22:16, 5 November 2023
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	[https://sourceforge.net/p/bibutils/home/Bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:		[https://sourceforge.net/p/bibutils/home/Bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

	* BibTeX -> MODS XML (<code>bib2xml</code>)		* to MODS XML:
	* Copac -> MODS XML (<code>copac2xml</code>)		** BibTeX -> MODS XML (<code>bib2xml</code>)
	* Endnote (Refer format) -> MODS XML (<code>end2xml</code>)		** Copac -> MODS XML (<code>copac2xml</code>)
	* Endnote (Endnote XML format) -> MODS XML (<code>endx2xml</code>)		** Endnote (Refer format) -> MODS XML (<code>end2xml</code>)
	* ISI Web of Science -> MODS XML (<code>isi2xml</code>)		** Endnote (Endnote XML format) -> MODS XML (<code>endx2xml</code>)
	* Pubmed XML -> MODS XML (<code>med2xml</code>)		** ISI Web of Science -> MODS XML (<code>isi2xml</code>)
	* RIS -> MODS XML (<code>ris2xml</code>)		** Pubmed XML -> MODS XML (<code>med2xml</code>)
			** RIS -> MODS XML (<code>ris2xml</code>)

			* from MODS XML:
	* MODS XML -> ADS (<code>xml2ads</code>)		** MODS XML -> ADS (<code>xml2ads</code>)
	* MODS XML -> BibTeX (<code>xml2bib</code>)		** MODS XML -> BibTeX (<code>xml2bib</code>)
	* MODS XML -> Endnote (<code>xml2end</code>)		** MODS XML -> Endnote (<code>xml2end</code>)
	* MODS XML -> ISI Web of Science (<code>xml2isi</code>)		** MODS XML -> ISI Web of Science (<code>xml2isi</code>)
	* MODS XML -> Reference Manager/RIS (<code>xml2ris</code>)		** MODS XML -> Reference Manager/RIS (<code>xml2ris</code>)
	* MODS XML -> Word 2007 XML Bibliography format (<code>xml2wordbib</code>)		** MODS XML -> Word 2007 XML Bibliography format (<code>xml2wordbib</code>)

	Bibutils is available for various platforms and can be downloaded as source code from the [https://sourceforge.net/projects/bibutils/files/ Bibutils home page] or. Older Bibutils versions are available as binaries from the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be downloaded for various [https://pkgs.org/download/bibutils Linux distributions] or installed via platform-specific package management systems:		Bibutils is available for various platforms and can be downloaded as source code from the [https://sourceforge.net/projects/bibutils/files/ Bibutils home page] or. Older Bibutils versions are available as binaries from the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be downloaded for various [https://pkgs.org/download/bibutils Linux distributions] or installed via platform-specific package management systems:

WikiSysop: Update external links

2023-11-05T20:09:43Z

Update external links

← Older revision		Revision as of 22:09, 5 November 2023
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	== About Bibutils ==		== About Bibutils ==

	[~~http~~://~~www~~.~~scripps.edu~~/~~~cdputnam~~/~~software~~/~~bibutils~~/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:		[https://sourceforge.net/p/bibutils/home/Bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

	* BibTeX -> MODS XML (<code>bib2xml</code>)		* BibTeX -> MODS XML (<code>bib2xml</code>)
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	* Pubmed XML -> MODS XML (<code>med2xml</code>)		* Pubmed XML -> MODS XML (<code>med2xml</code>)
	* RIS -> MODS XML (<code>ris2xml</code>)		* RIS -> MODS XML (<code>ris2xml</code>)


	* MODS XML -> ADS (<code>xml2ads</code>)		* MODS XML -> ADS (<code>xml2ads</code>)
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	* MODS XML -> Word 2007 XML Bibliography format (<code>xml2wordbib</code>)		* MODS XML -> Word 2007 XML Bibliography format (<code>xml2wordbib</code>)

	Bibutils is available for various platforms and can be downloaded as ~~binaries or~~ source code from the [~~http~~://~~www.scripps~~.~~edu~~/~~~cdputnam~~/~~software~~/~~bibutils~~/ Bibutils home page] or the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be installed via platform-specific package management systems:		Bibutils is available for various platforms and can be downloaded as source code from the [https://sourceforge.net/projects/bibutils/files/ Bibutils home page] or. Older Bibutils versions are available as binaries from the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be downloaded for various [https://pkgs.org/download/bibutils Linux distributions] or installed via platform-specific package management systems:

	* [~~http~~://gentoo~~-portage~~.~~com~~/app-text/bibutils Gentoo Linux]		* [https://packages.gentoo.org/packages/app-text/bibutils Gentoo Linux]
	* [~~http~~://~~club~~.~~mandriva~~.~~com~~/~~xwiki~~/~~bin/view/KB/Bibutils Mandriva Linux~~]		* [https://formulae.brew.sh/formula/bibutils Homebrew]
	* [~~http~~://~~www~~.macports.org/~~ports.php?by=name&substr=~~bibutils MacPorts]		* [https://ports.macports.org/port/bibutils/ MacPorts]

	== refbase integration with Bibutils ==		== refbase integration with Bibutils ==

WikiSysop: Update link to Community_portal page

2023-11-05T17:53:16Z

Update link to Community_portal page

← Older revision		Revision as of 19:53, 5 November 2023
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	UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";		UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

	[[refbase:~~Community_Portal~~\|Let us know]] if you run into problems.		[[refbase:Community_portal\|Let us know]] if you run into problems.

	[[Category:Installation]]		[[Category:Installation]]
	[[Category:Requirements]]		[[Category:Requirements]]
	__NOEDITSECTION__		__NOEDITSECTION__

WikiSysop: Hide section edit links

2023-11-05T17:42:04Z

Hide section edit links

← Older revision		Revision as of 19:42, 5 November 2023
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	[[Category:Installation]]		[[Category:Installation]]
	[[Category:Requirements]]		[[Category:Requirements]]
			__NOEDITSECTION__

WikiSysop: Original page content from 23-Jan-2009

2023-11-05T17:41:29Z

Original page content from 23-Jan-2009

New page

This page describes the refbase integration with Bibutils.

== About Bibutils ==

[http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* BibTeX -> MODS XML (<code>bib2xml</code>)
* Copac -> MODS XML (<code>copac2xml</code>)
* Endnote (Refer format) -> MODS XML (<code>end2xml</code>)
* Endnote (Endnote XML format) -> MODS XML (<code>endx2xml</code>)
* ISI Web of Science -> MODS XML (<code>isi2xml</code>)
* Pubmed XML -> MODS XML (<code>med2xml</code>)
* RIS -> MODS XML (<code>ris2xml</code>)

* MODS XML -> ADS (<code>xml2ads</code>)
* MODS XML -> BibTeX (<code>xml2bib</code>)
* MODS XML -> Endnote (<code>xml2end</code>)
* MODS XML -> ISI Web of Science (<code>xml2isi</code>)
* MODS XML -> Reference Manager/RIS (<code>xml2ris</code>)
* MODS XML -> Word 2007 XML Bibliography format (<code>xml2wordbib</code>)

Bibutils is available for various platforms and can be downloaded as binaries or source code from the [http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils home page] or the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be installed via platform-specific package management systems:

* [http://gentoo-portage.com/app-text/bibutils Gentoo Linux]
* [http://club.mandriva.com/xwiki/bin/view/KB/Bibutils Mandriva Linux]
* [http://www.macports.org/ports.php?by=name&substr=bibutils MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the <code>safe_mode</code> setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the <code>safe_mode_exec_dir</code> setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils". This approach requires that your web server is configured to follow symlinks.

% ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace <code>/path/to/bibutils/</code> with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (<code>\path\to\bibutils\</code>). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_Portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]