Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Citation and reference managers for Linux: short overview

    29th October 2008

    For some period of time, I had to switch to my Windows installation when writing articles with references, because I keep my references database there and there is an extremely convenient add-on for MS Office to insert citations and format bibliography on the fly.

    However, it is quite inconvenient to make/run programs/scripts under Linux, and then switch to Windows to describe the obtained results in the article-like form. Thus, I briefly investigated available citation managers for Linux.

    Note: this is just a review at the moment, I hadn’t tried yet the options described.

    Update. For the sake of completeness: I’ve settled with Zotero quite a while ago, and had no need to look for alternatives. Default storage size for full texts in Zotero eventually became too small for me, so I found a free web-storage with WebDAV interface, and configured Zotero to use it. I have also heard positive feedback about Mendeley, but haven’t tried it myself. Finally, I was recently contacted by the developers of paperpile.com – a Chrome extension for reference management. The most interesting features are integration with Google Docs (where you can insert citations, including shared documents) and Google Drive (where the full-text PDFs are stored). I haven’t tried it, though; there is a free 30-day trial.

    First comes the Zotero+OpenOffice Writer, as suggested by sybille (edited quote):

    Zotero includes support for an extension for OpenOffice.org Writer.

    There’s a lot of great documentation about Zotero at the home page for the extension, including various useful demos of its features.

    If you want the newest version of Zotero, it’s better to install it from that page rather than the official Firefox add-ons site.

    Once you’ve installed Zotero, you can install the extension for OpenOffice.org as follows: first download the extension from the Zotero site. Unzip the file so that you have a file called Zotero.oxt somewhere where you can find it. Then open a new text document with ooWriter, go to Tools -> Extension Manager, choose “Add.” Navigate to the directory where you put Zotero.oxt and choose it. Once the extension installs, restart Writer, and now you’ll see a new toolbar for inserting references and bibliographies into your Writer documents.

    I prefer Zotero because it makes it so easy to enter bibliographical information into the database it manages. Generally it’s just a matter of locating the publication or resource you want to cite in an online library or journal service (some newspapers are currently supported as well), and then clicking on an icon in the Firefox address bar. Maybe some small edits are needed depending on how the information is imported, but that’s it.

    Zotero also allows taking notes and adding/annotating attachments – links to files, copies of files, snapshots of web pages, etcetera etcetera. There are some new full-text search capabilities as well.

    The OpenOffice extension does the same kind of job as Bibus, using UNO service to insert citations and bibliographies from Zotero into Writer documents in any number of styles (currently over 1100). These references can be updated when the Zotero database changes.

    I’m finding the Firefox/Zotero combination very useful for my research, and I think this setup is worth a look for anyone doing research.

    Zotero summary: easy references database maintenance and import into; has bibliography formatting capabilities with over 1100 styles; has OpenOffice extension; seems to have RefMan/EndNote import feature (not verified). This is the first candidate to be tried, even without looking into other options.

    Bibus:

    Bibus is a bibliographic and reference management software. As with other such tools, Bibus allows one to search, edit, and sort bibliographic records. In addition, Bibus contains features that makes it unique among open source and even commercial bibliographic databases:

    * Hierarchical organization of the references with user defined keys
    * Designed for multiuser environments
    o You can share the database between an “unlimited” number of users
    o Each user will have its own classification
    o You can define read-only and read-write users
    * Live queries; that is searches that update as the database changes
    * On-line PubMed queries
    * On-line eTBLAST queries
    * Insertion of references and formatting of bibliographies into two widely used Word Processors (OpenOffice.org and Microsoft Word)
    * Foreign language support through Unicode and gettext. As of version 1.4, Bibus is available in English, Chinese, Czech, French, German, Hungarian, Portuguese, Slovenian, Spanish.
    * Bibus works on most modern platforms:
    o Gnu/linux with OpenOffice.org
    o Windows98/2000/XP with OpenOffice.org and Microsoft Word
    o On other platforms (MacOS X, …) Bibus works with Microsoft Word but styles cannot be created at this point (this should change soon for MacOS X)

    Bibus summary: single integrated solution for managing references and citations. Based on the description only, looks on par with Zotero (if not superior to). However, nothing is said about the ease of importing new citations. Has Debian package, so this is already installed and ready to try it out (simultaneously with Zotero, which is now also installed). One more theoretical benefit of Zotero might be in it’s cross-computerability, meaning that simple synchronization of FireFox add-ons might also synchronize your references, which is a great plus (need to investigate that). Bibus, on the other hand, uses local SQLite database, which adds bits of hassle when there is a need to keep several workstations in sync.

    Jorge:

    Jorge is an OpenSource bibliography management software entirely written in Java. It will provide an free alternative to professional bibliography management software like EndNote©.

    In the first step you will be able to create your own literature database. From this literature database you can create citation lists and export them to BibTeX or plain text formats. The database itself will be an XML-File as the saveable citation lists will be.

    In a second step I try to implement an search interface to the Z39.50 protocol libraries. This is for to connect to public libraries via the ISO Z39.50 protocol. With this search you will be able to access a wide variety of libraries via the internet and import search results to your local database.

    Jorge summary: has an interesting motivation behind the name of the software; I dislike Java-software, so won’t try this one until others prove to be insufficient.

    Referencer

    Referencer is a Gnome application to organise documents or references, and ultimately generate a BibTeX bibliography file. Referencer includes a number of features to make this process easier:

    * Smart web links
    Referencer uses documents’ metadata to provide handy links to the document’s web location — no need to maintain your own bookmarks.
    * Import from BibTeX, Reference Manager and EndNote
    No need to start from scratch — Referencer will import your existing bibliography files using the BibUtils library.
    * Tagging
    No need to organise your documents into rigid directory trees — with Referencer you can use tags to categorise your documents.
    * Automatic arXiv, PubMed and CrossRef metadata retrieval
    If you show Referencer a PDF which has an arXiv ID or DOI code, Referencer will retrieve the metadata for this document over the internet.
    * Python plugin support
    Referencer can be extended using the versatile Python scripting language.
    * Localisation
    Referencer is translated into many languages.

    Referencer summary: can insert citations into LyX documents; uses BibTex, which I believe is a good thing ;) ; has tagging and import from online sources; is present in Debian testing repository; is suitable for those used to working with LaTex; this is an option to try, but for me personally requires time investments into learning Lyx/LaTex/BibTex, so this goes after Zotero and Bibus in my personal rating (it would go first, if I had LaTex experience).

    JabRef:

    JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.5 or newer), and should work equally well on Windows, Linux and Mac OS X.

    BibTeX is an application and a bibliography file format written by Oren Patashnik and Leslie Lamport for the LaTeX document preparation system. General information about BibTeX.

    Bibliographies generated by LaTeX and BibTeX from a BibTeX file can be formatted to suit any reference list specifications through the use of different BibTeX style files. We support this initiative to build a searchable database of BibTeX style files, organized by journal names: LaTeX bibliography style database.

    # Detailed editing of BibTeX entries.
    # Search a pattern in the whole bibliography.
    # You can group entries explicitly, by keywords or any other fields.
    # Import: BibTeXML, CSA, Refer/Endnote, ISI Web of Science, SilverPlatter, Medline/Pubmed (xml), Scifinder, OVID, INSPEC, Biblioscape, Sixpack, JStor and RIS.
    # Export: HTML, Docbook, BibTeXML, MODS, RTF, Refer/Endnote and OpenOffice.org.
    # You can add your own fields to any BibTeX entry type.
    # Launch external applications: PDF/PS viewers, web browser, insert citations into LyX, Kile, LatexEDitor, Emacs, Vim and WinEdt
    # Search Medline, Citeseer, IEEEXplore and arXiv
    # Support for XMP Metadata in PDFs
    # Improve the workflow of sharing PDFs and bibliography information
    # Plugin functionality

    JabRef summary: similar to Referencer, but in Java. Would fit cross-platform BibTex-ers. Will not be further considered.

    Sixpack: last updated in 2004, listed for completeness.

    Feel free to comment about your best experience with reference/citation managers on Linux. Also, feel free to suggest new entries for the list above.

    Share

    One Response to “Citation and reference managers for Linux: short overview”

    1. Websites tagged "bibtex" on Postsaver Says:

      [...] – Citation and reference managers for Linux: short overview saved by omifan922009-03-27 – [...]

    Leave a Reply

    XHTML: You can use these tags: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>