Slides for a hands-on Zotero workshop

One of the key tasks scientists need to master is how to manage bibliographic information: collecting relevant literature, building a digital library, and handling citations and bibliographies during writing.

This tutorial introduces Zotero (www.zotero.org), an easy to use reference management tool made by scholars for scholars. The tutorial covers the basics of using Zotero for collecting, organizing, citing and sharing research. Zotero automates the tasks of managing bibliographic data, storing and renaming PDFs, and formatting references. It also integrates with widely used text processors, and can synchronize your library across devices. There is no more need to search through disorganized file folders full of inscrutably named PDF files, to copy and paste references across documents, or to manually deal with pointless differences in citation styles. Ultimately, the point of using a reference manager is to free more time for real research.

Note: these are slides made for a hands-on workshop. They may not work well outside the context of a live Zotero demonstration. I share them because they may still contain some useful information.

Who will write a lightweight duplicate detection plugin for Zotero?

Duplicate detection is one of the things any serious reference manager should offer. Zotero users have been clamouring for it since the early days. There are basically two ways to implement it: as a preflight check, warning the user when they are about to add a potential duplicate; and as an after the fact scan, which enables users to weed duplicate items from their library.

The most recent version of Zotero takes the second route: a posthoc duplicate detection mechanism. Though definitely better than nothing, and with an elegant merging solution, the interface is still far from perfect and yields a lot of false positives, making it somewhat difficult to use. Besides, it is slow, because it tries to compare everything with everything, which amounts to a huge amount of operations even in moderately sized libraries. Although it is good to have at least something, what seems to me have been overlooked is that prevention is better than cure, and that a quick check before adding new items to the library would help users a lot.  Continue reading

Zotero for Chrome and Safari

Here’s a quick tip for Zotero users who like to do their browsing in Chrome or Safari: you can install “Zotero Connectors” that will make Zotero recognize references in Chrome and Safari just like in Firefox. The Zotero developers are working on a standalone version, but these connectors can already talk to your Zotero library in Firefox. So if you, say, find yourself going to Chrome for its speed and nice interface, you can simply connect it with Zotero and use Firefox to host your local Zotero library until Zotero Standalone comes along. Continue reading

Unified Style Sheet for Linguistics Journals

Not all linguists may be aware of this, but since 2007 there has been a Unified Style Sheet for publications in our field, developed by the editors of a number of linguistic journals, including Language. (Oddly enough, just which journals besides Language joined in the effort remains unclear.) There is not much centralized information available about this style, but we have the 2007 specifications (PDF) and a page endorsing the style at the official LSA website.

As Stephen Anderson writes on the Linguist List,

Use of this style is encouraged, and if it is widely adopted, that could considerably facilitate the preparation of manuscripts. In support of that, it would be useful to have software support for it in popular document preparation systems.

I’m happy to report that Zotero now supports the unified style through the powerful open format CSL. If you have Zotero, you can simply install the style right away. Zotero of course already supported lots of other citation styles, including the widely used APA and MLA as well as styles for specific journals like Language (install) and the Journal of Pragmatics (install).

I haven’t been able to find a definitive list of the journals that have adapted the Unified Style Sheet for Linguistics, but some examples of journals using and/or endorsing it are Language itself, Semantics & Pragmatics, and the Journal of English Linguistics. Also, the LDLT conference series at SOAS, London is using it in its proceedings. Does anyone know of more journals?

Zotero 1.5 is here: synchronization and tons of other features

It’s here. Zotero 1.5 beta. The new version comes with built-in synchronization, exports to more than 1100 citation styles, and supports browsing your library online (see below). Zotero is now better than EndNote on all fronts. Here’s a quick overview of the most important features:

  • Synchronization. Automatically keep your library in sync across different PCs. If you have access to WebDAV storage, synching can also include your attachments.
  • Automatic backup. A copy of your library is stored safely on the synchronization server.
  • More than 1100 CSL citation styles. The style repository has grown immensely due to community efforts. Zotero styles are built on the powerful open source Citation Style Language (CSL), an XML dialect.
  • Support for EndNote styles. Thousands of EndNote .ens styles can now be used for citation formatting. These styles are available to licensed users of EndNote.
  • Rich text notes. Formatting can now be applied to notes with a WYSIWYG editor.
  • Automatic detection of PDF metadata. Another much requested feature. Not yet bulletproof because it depends on the information available in your PDF and the repository used to look it up, but a great step forward.
  • Shared collections. Easily share and build collections with colleagues.

All of this built on open source technologies and standards, which means that your data is not locked up in proprietary software at the mercy of profit driven companies.

New website features

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Browse your Zotero library online [click for fullsize]

Meanwhile, the Zotero website has seen a major revamping, the most important new feature being the ability to browse your library online. Other features are more geared towards social networking activities: users now can have an online Zotero profile, can follow other Zotero users, and can build an online CV.

If you’re still stuck on EndNote, check out making the switch to Zotero, or see my review and comparison from last year. Questions? There are lots of helpful and friendly people hanging out in the Zotero forums. You can also post them below.

12 must know Zotero tips and techniques

Zotero is getting better and better. In a while, version 1.5 will bring synchronization, online backup of your library, +1100 CSL citation styles, and PDF metadata extraction (for the daring, a sync preview version is available). But even in its current incarnation Zotero is easily one of the best bibliographic managers out there. Here are twelve tips and tricks that help you to get the most out of it.

  1. Drag files from the web right into your library
    Got a reference in your library, but no PDF? Or saved an item from a repository which doesn’t provide a fulltext version? Do a quick search for the title on Google Scholar — it is good at finding PDFs on author’s webpages. If you find one, just drag the link from the page onto the reference in your library. Zotero stores and attaches the PDF for you.
  2. Enter a series of items by duplicating a template
    Adding a series of related references to your library? Start with one item for which you fill in the fields that are the same for all items (e.g. editors, book title, year, publisher, place) and duplicate it (Right-click > Duplicate item). Then fill in the particularities.
  3. Quick Copy a citation using Ctrl+Shift+C or drag and drop
    Sending a PDF to a colleague, or mentioning a reference somewhere? Quickly copy the citation by selecting the reference and pressing Ctrl+Shift+C (Cmd-Shift-C on the Mac), or simply drag it from Zotero onto any edit window (for example a new email). The default output style can be specified under Preferences > Export; the shortcut key can be customized under Shortcut keys.
  4. Have Zotero index your PDFs
    Zotero can index your PDF attachments and make them fully searchable, turning your library from a mere linked catalogue into a Google Books of sorts. The option is turned off by default because it relies on an external open source program (pdf2txt) which is not distributed with Zotero. However, Zotero can automatically install it and enable fulltext indexing: simply go to Preferences > Search and click on the ‘Check for installer’ button. For more info see pdf fulltext indexing in the Zotero documentation.
  5. Start quicksearch with ” to trigger advanced search
    By default, Zotero starts searching when you put the first few characters in the Search box. In a large library with fulltext indexing enabled, this can be tiresome (you wanted to look for “statistical methods”, but Zotero locks down searching for “st”). To avoid this, start your search with ” (double quote) to have Zotero wait until you finish typing and hit enter.
  6. Press Ctrl to find out in which collections an item is
    Looking at an item in your library and wondering whether you already categorized it? Press Control and Zotero will highlight the collections in which it is contained.
  7. Relocate your Zotero folder to a more sensible place
    The default place for the Zotero database and attachments in right in your Firefox profile, which isn’t the easiest to locate whichever OS you are on. Go to Preferences > Advanced to customize the storage location. You can place it in a folder that is included in your regular backup schedule or put it on a portable drive so that your library always travels with you (tip: if you work a lot on shared computers, combine it with Firefox Portable, which you can even use without administrator rights).
  8. Keep track of recent additions using a saved search
    Often you add new items without worrying about tagging or putting them in collections. Click Advanced search, select “Dated Added” > “is in the last” > X “days/months” and fill in the desired period; then save the search. This gives you a dynamically updated overview of your latest additions, so that you can go back to them and do the categorization and tagging work when it suits you.
  9. Tag multiple items at once
    Want to tag multiple items at once? Select them, make sure the tag selector is visible in the left pane, and drag them onto the tag you want to use. The tag will be applied to all items.
  10. Tag incomplete items to find them back and fix them later
    Sometimes you know an item has incomplete metadata (e.g. missing page numbers or publisher), but you don’t have the time to fix it right away. Make it a habit to tag such items (“needs metadata”) when you see them. Now you can find them and fix them whenever you have some time to kill.
  11. Use a separate folder for files to be ingested
    Someone gives you a bunch of PDFs to read; or you download a paper somewhere without having the metadata handy. Make it a habit to save such files in a subfolder /new/ in your Zotero folder. Then once in a while go through that folder. Do a quick search for the title on your favourite repository, grab the metadata, and then drag the PDF from your filemanager onto the reference in Zotero. Much better than having those loose PDFs scattered all over your hard drive (or in your mailbox!) — and it helps you keep track of your reading history too.
  12. Display a timeline to visualize your bibliography
    Not a feature you’ll use everyday, but a neat one nonetheless: Zotero can display your library, or portions of it, on a timeline. Select a group of references, a tag, or a collection and click ‘Create timeline’ (in the Gear menu). This gives you an overview of the items in time. Now you have to ask yourself: is the recency bias due to your reading habits or is it really true that most of the research was done in the last twenty years? (Probably a bit of both.)

Questions or suggestions? Leave a comment.

Zotero Sync Preview

Exciting news for Zotero users: synchronization has arrived. After some months of closed beta-testing, a public Sync Preview version was released recently. This means that Zotero users can now automatically synchronize their libraries across computers and even across platforms.

Although there are still some minor wrinkles, the sync functionality works perfectly fine and there are some exciting new features, including the possibility to import thousands of Endnote styles. With the import functionality comes a handy style manager, another step towards an elegant, shared, and open source solution to citation styling. That’s two killer features in one release — impressive work by the Zotero folks.

Also note the following:

Before Zotero 1.5 ships, we will add functionality to allow users to synchronize attachments to their own servers or other storage space (and we’ll also provide a hosted storage solution for all Zotero users). [forum post by Sean Takats]

Do keep in mind that the current preview is a preliminary version intended for public testing; do not expect it to be bug-free. Always make a backup copy of your full Zotero folder and try the Sync Preview in a new profile (step-by-step instructions on the sync preview page). Easier yet, download Firefox 3 Portable and try out Zotero Sync Preview 1.5 on a copy of your library without risking data loss or profile mixups. If your workflow is fine without synchronization, my advice is to avoid the growing pains of the preview version and wait until the release of the official 1.5 version, which should follow within a few months.

Not sure what Zotero is? Check the website or read my review of it.

The etymology of Zotero

If you’ve read yesterday’s post (Zotero, an Endnote alternative) or come across Zotero elsewhere, you may have been wondering about its name. I believe most Anglophones pronounce the word [ˌzɔˈtɛɹoʊ] (zoh-TER-o), but the term itself actually derives from the Albanian verb zotëro-j [zɔtərɔj] ‘master, acquire’. The final -j marks the 1st person indicative (the regular citation form for Albanian verbs); in the imperative, we would get the bare verb root zotëro [zɔtərɔ]. Such subtleties did not figure in the initial baptismal act though, as we learn from the following transcript of a podcast featuring the people behind Zotero:

The web being what it is, I just quickly googled and found an English-Albanian dictionary and typed a bunch of our keywords that we associated with the project and when I typed in ‘learning’, uhm… one of the variants was ‘to learn something extremely well, that is to master or acquire a skill in learning’ was “zotëroj” [pronounced [ˌzɒˈtuəɹʏdʲ] by DC, MD] (laughs), which we have shortened, we took of the -j at the end which is more of a ‘y’-sound and uh we took off the umlaut …
(Dan Cohen, Library Geeks Podcast 5, 22:48—25:15)

It’s that simple. And for good reason: essentially, want you need in branding is a name that sticks but at the same time is not too common; if it makes some sense (as ‘Zotero’ does), that’s even better. The main reason for choosing an Albanian word was thus quite simply to minimize namespace competition. It could have been any other language — in the podcast, Cohen mentions Maori; Hawaiian is another popular one (wikiwiki), and Bantu languages do well too (cf. Ubuntu, a trendy Linux distribution).

Will It Brand?

Well, not really any other language of course — a quick glance over the newest web 2.0 names shows that the preferred languages for this kind of stuff seem to be those with simple phonotactics, a preference for open syllables, a basic 5 vowel system, and not-too-outlandish consonant inventories. So at least in the Zotero case, Siwu is out of luck with suã ‘learn’ (nasal vowel penalty); as is Tamashek with əlmæd ‘learn, acquire’ (muddy vowels and a voiced coda, tsk); as is Ibibio with kpéép ‘learn, acquire’ (a labio-velar stop, for petes sake!); readers are no doubt able to come up with better examples.

Fortunately, these need not be fatal problems. Dan Cohen’s account shows that if it doesn’t fit, we can always make it fit; just chop off needless morphology and diacritics and you’re good to go. Now Albanian, hitherto an obscure 6 million speaker language making up it’s own branch of Indo-European, enjoys celebrity status as the language that endowed the Next-Generation Research Tool with a worthy name. Come to think of it, who would not like to sacrifice some orthographic blunt for publicity’s sake? Suddenly all those woefully inadequate orthographies we linguists have been cursing at are beginning to make sense! Next time the underspecified orthography drives you nuts again, find a product in need of a name and monetize your despair. I’ve heard naming consultants easily make twice as much as linguists.

P.S. A great resource on naming is Nancy Friedman’s Away With Words, which I found via the posting on Web 2.0 names referenced above.

Zotero, an Endnote alternative

I wasn’t planning to make this a software weblog, but I’ll make an exception for Zotero because I think fellow researchers will find it an interesting tool. Zotero [ˌzɔˈtɛɹoʊ] is a free piece of software that lives in your browser, helping you to ‘collect, manage and cite your research sources’ in all sorts of beautiful ways. It bills itself as The Next-Generation Research Tool, and in this post I’ll try to explain why I think that’s true. The background to this posting is that I made the move from Endnote to Zotero two months ago — and I have never since considered going back.

It all started when I upgraded from Endnote 7 to Endnote X to get Unicode support. Endnote X included Endnote Web, a web-based implementation that looked interesting. I had some difficulty getting the two to work together, and when I finally did, there were drawbacks that made me look out for an alternative. A Google search led me to Zotero, which was a breeze to install. I could simply import my Endnote library and started a testdrive. Within minutes I was totally hooked. The Zotero interface offered everything I had been missing in Endnote and then some. What makes Zotero so good?

Seamless integration with online research

First of all, Zotero answers the needs of researchers in the digital age. The rise of online repositories like JSTOR, ProQuest, SpringerLink, and Google Scholar has caused a shift in our research habits; we spend more time browsing virtual libraries, and less time hanging around in physical ones. Zotero seamlessly integrates with this online experience by automating the wearisome labour of saving references and by offering many ways to manage and enrich the data thus collected. All from within the web browser. Continue reading