Software I like: Zotero

Get Zotero

Zotero ‘is a free, easy-to-use tool to help you collect, organize, cite, and share research’, providing integration with word processors (including LibreOffice/OpenOffice Writer) and Web browsers.

From the Zotero Web site, download Zotero itself; the Zotero Connector for your Web browser; and a word-processor plugin. The last two may be installed more or less automatically as part of the installation of Zotero itself.

A change log is available.

(Before Zotero 5, there was an extension specifically for Firefox (Zotero for Firefox) but it stopped working as of Firefox 57 (ref).)

Zero-cost alternatives include Mendeley (proprietary, by Elsevier) and Docear, among many others. See this comparison of reference management software. As of 2015 Feb 16, those that are shown as being FLOSS, having OO/LO integration, and having stable releases within 2014 or 2015, include JabRef (a 'Java BibTeX manager') & Zotero. (The tables in the comparison are not necessarily up-to-date or accurate. On 2015 Feb 16, for Docear I changed Yes to No for integration with OO/LO and Kile/LyX, and updated the latest release for Zotero from 2014 Apr 30 to 2015 Feb 11, with intervening releases having happened in Jun, Sep, Oct, Dec & Jan.)

My notes

Zotero can pull bibliographic information from a wide variety of Web pages. See here for a list of currently recognized Web sites, and information about how to add new sites.

If Zotero recognizes something that it can capture from a Web page, a capture icon appears in the Firefox address bar. There are several different capture icons, indicating whether there is a single item to be captured (book Zotero Book icon, article Zotero Article icon, Web page Zotero Web-page icon, image Zotero Image icon etc.) or multiple items Zotero Folder icon. Click on the capture icon to capture the item(s).

Zotero plugins are available for a wide variety of software, including LibreOffice/OpenOffice. (As of 2013 Aug 18, Zotero does not support Apache OpenOffice 4 but this has changed in the development version (ref). At the moment Zotero supports AOO version 3 but recommends LibreOffice.)

Zotero supports syncing from one computer to another, and public and private groups. One can browse one's library on the Zotero server by logging in to the Zotero Web site and clicking on My Library. Click on Settings at the top, next to Welcome, username, to edit the user profile, check how much storage is being used, etc.

Both bibliographic information and actual documents can be stored on the Zotero server, but it costs money for more than a small collection of documents. phpZoteroWebDAV 2.0 by Christian Holz is a PHP script for storing a collection on one's own Web server (see also Mark Sample's discussion).

Zotero currently (2011 Apr 29) cannot pull items from an Ovid search-results page (discussion). An alternative is to select the desired items (or select all items) and export in RIS format, then import that into Zotero, which will create a new collection. (This was fixed as of 2012 Mar 17.)

It is (or was) recommended that you turn off recording of changes, at least when debugging, because it was ‘known to cause problems with Zotero integration’. This has improved somewhat but may still cause some problems. For one thing, when changes are being recorded and a citation is deleted, the corresponding item will still appear in the bibliography even after a Zotero refresh is done.

There is a buggy interaction between Zotero and some experimental features of LibreOffice 3.5 (ref).

Installation and reinstallation

To begin, or when things have stopped working properly:

If things don't work, mix in some exits and restarts of Firefox, your word processor and/or your operating system. Sometimes ‘not working’ will mean nothing happens when you try to insert a citation, and sometimes it will mean nasty error messages.

Collections

An item in a Zotero library (‘My Library’) can be assigned to one or more collections. Dragging an item from one collection to another causes it to be copied; there is no one-step method of moving an item from one collection to another, you must copy and then delete the original item.

Collections can contain sub-collections. To make it appear as though items in a sub-collection are also in the parent collection, go to about:config in Firefox, find extensions.zotero.recursiveCollections and set it to true.

To see which collections an item is in, select the item in the middle pane and then hold down (don't just click quickly) the Alt key (Unix), Control key (MS Windows) or Option key (Mac). All collections that contain the selected item will be highlighted in the left pane.

Edit Citation feature

The Zotero Edit Citation icon can be used for a number of neat things. For example:

Paragraph style for bibliography

Zotero uses a specific paragraph style (e.g., Bibligraphy 1) for the bibliography. If you are using a document template that has a pre-defined paragraph style for the bibliography (e.g., Reference), you can follow these steps in LibreOffice to modify the style used by Zotero to match the one used in the template:

  1. Do Format ▶ Styles and Formatting to open the Styles and Formatting dialogue box.
  2. Right-click on the Bibligraphy  style and select Modify.
  3. In the Organizer tab, under Linked with (or Inherit from) specify the pre-defined paragraph style for the bibliography (e.g., Reference).
  4. Click on the Standard button to make the definition of the Bibliograph 1 style the same as that of the pre-defined style (e.g., Reference).

Unfortunately, it seems that this must be redone whenever the bibliography is refreshed because Zotero redefines its paragraph style.

Citation styles

Citation styles (defining what both the in-line citation and the reference-list entry look like) are defined in Zotero using CSL. Styles can be selected from the Zotero Style Repository.

A citation style can be adjusted by editing the .csl file. See instructions for editing styles, which discusses alternative approaches, and also a tool for finding CSL citation styles by name or by example and then using either a visual editor or a more conventional editor with immediate feedback.

To install a style from a .csl file on your computer, in Zotero do Edit ► Preferences ► Cite ► Styles, click on the Plus sign, browse to find the .csl file, select it, and click on Open.

As of 2021 Aug 28, the latest version of CSL is 1.0.1, released 2012 Sep 3 (ref). This version is backward compatible (‘with minor exceptions’) with version 1.0 (released 2010 Mar 22) but it is not backward compatible with the previous 0.8 format (released 2009 Mar 21). A tool is available for automatically converting version 0.8 to version 1.0. The tool involves using an XSLT processor; I've done it (2018 Aug 16) using xsltproc, with a command like
xsltproc -o name_1.0.csl csl_update.xsl name.csl

On-line validators for CSL can be found at validator.citationstyles.org and simonster.github.io. I had better luck with the former.

My styles

For my reference, and as examples of the many possibilities, the following sections describe the changes I made to an old APA style file (from 2011, CSL version 0.8) when creating my cihr.csl style file (since converted to CSL version 1.0 and further modified).

Citations with multiple authors

The APA citation style specifies the use of et al. for six or more authors. To change it to three or more, set the et-al-min attribute to 3 in the <citation …> element.

Author's initials in citations

When using a style like APA for which the authors' initials normally don't appear in a citation, sometimes they will appear if Zotero feels that it's necessary to disambiguate the names of authors with the same surname. Sometimes this is because the same author's name appears in different forms in the database, and sometimes it's because there really are two different authors with the same surname but different given names. And sometimes the disambiguation is really appropriate and sometimes Zotero may make a mistake (discussion). Either way, if you want to avoid having the initials appear, remove the attribute disambiguate-add-givenname="true" if it is present.

Additional authors' names in citations

Given two references, 'auth1, auth2, auth3 (1980)' and 'auth1, auth2, auth4 (1980)', when cited together they will produce '(auth1 et al. 1980a, 1980b)' only if the attribute disambiguate-add-names="true" is not present.

DOI

The Zotero APA style includes a DOI if given, even if the journal name, volume and pages are also given. Inclusion of the DOI can be suppressed by removing the lines

<if variable="DOI">
<text variable="DOI" prefix=…/>
</if>
and removing or revising any affected choose and else elements.
Short form of journal title

To force the journal title to be given in its short (abbreviated) form, add form="short" to the <text variable="container-title"/> element.

Bibliography format for many authors

The number of authors to include in a bibliography entry can be increased by adjusting the attributes et-al-min and et-al-use-first in the <bibliography …> element. Adding et-al-use-last="true" causes the last author’s name to be included after an ellipsis character ().

Bibliography line spacing

Line spacing in the bibliography is controlled by the attributes line-spacing (within bibliographic entries) and entry-spacing (between bibliographic entries).

Multiple numeric citations

If two or more references are cited together numerically, the IEEE style is ‘[1][2]’, and if one wants to add ‘e.g.’ in front it would have to be something like ‘(e.g., [1][2])’, which is ugly. Apparently IEEE is the only format that does this (ref.). The Springer Basic style, for example, gives ‘[e.g. , 1, 2]’, with the ‘e.g.’ inside the brackets but with an unwanted space. The Vancouver style gives ‘(e.g. ,1,2)’ with the same unwanted space and a missing wanted space.

Data storage

See here for where Zotero stores things. By default, under MS Windows it's something like
C:\Documents and Settings\username\Application Data\Mozilla\Firefox\Profiles\random.default\zotero
and under *n*x it's something like
~/.mozilla/firefox/random.default/zotero

Zotero can import and export bibliographic data in a number of formats.
Field equivalences (incl. proposal for my Ref)
Zotero GUI Note Abstract Tag Extra
Zotero RDF bib:Memo dcterms:abstract dc:subject dc:description
Bibtex comment abstract keywords note
RIS (Refman) Nn Nn KW n/a
Ref KW BS

Formatted citations and bibliographies

The following table illustrates some of the citation and bibliography styles included with Zotero 1.0.6. Some additional styles are available here.

For hyphenated given names, all of the styles here that use initials drop the hyphen and the following initial.
Formats
Am Med Assoc 1-3

1. Nicholson DT, Chalk C, Funnell WRJ, Daniel SJ. Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model. Medical Education. 2006;40(11):1081-7.

 

2. Ladak HM, Funnell WRJ, Decraemer WF, Dirckx JJJ. A geometrically nonlinear finite-element model of the cat eardrum. J. Acoust. Soc. Am. 2006;119(5 Pt 1):2859-68.

Chicago A-D A Y

Ladak, Hanif M, W Robert J Funnell, Willem F Decraemer, and Joris J J Dirckx. 2006. A geometrically nonlinear finite-element model of the cat eardrum. The Journal of the Acoustical Society of America 119, no. 5 Pt 1 (May): 2859-68. doi:16708944.

 

Nicholson, Daren T, Colin Chalk, W Robert J Funnell, and Sam J Daniel. 2006. Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model. Medical Education 40, no. 11 (November): 1081-7. doi:MED2611.

Harvard A Y

Ladak, H.M. et al., 2006. A geometrically nonlinear finite-element model of the cat eardrum. The Journal of the Acoustical Society of America, 119(5 Pt 1), 2859-68.

 

Nicholson, D.T. et al., 2006. Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model. Medical Education, 40(11), 1081-7.

IEEE [1-3]

[1] D.T. Nicholson et al., "Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model," Medical Education, vol. 40, Nov. 2006, pp. 1081-7.

 

[2] H.M. Ladak et al., "A geometrically nonlinear finite-element model of the cat eardrum," The Journal of the Acoustical Society of America, vol. 119, May. 2006, pp. 2859-68.

NLM (1-3)

1. Nicholson DT, Chalk C, Funnell WRJ, Daniel SJ. Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model. Medical Education. 2006 Nov ;40(11):1081-7.

 

2. Ladak HM, Funnell WRJ, Decraemer WF, Dirckx JJJ. A geometrically nonlinear finite-element model of the cat eardrum. J. Acoust. Soc. Am. 2006 May ;119(5 Pt 1):2859-68.

Nature 1-3

1. Nicholson, D.T. et al. Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model. Medical Education 40, 1081-7(2006).

2. Ladak, H.M. et al. A geometrically nonlinear finite-element model of the cat eardrum. J. Acoust. Soc. Am 119, 2859-68(2006).


R. Funnell
Last modified: 2022-05-02 11:58:06