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How to Get Organized With Reference Managers for Science – Zotero

A table with stacked document wallets and folders to represent the reference manager Zotero

My previous posts have discussed the features of several reference managers, some of which are free and others that are paid. Last, but certainly not least, I would like to draw your attention to another free software, Zotero (pronounced zoh-TAIR-oh).

Originally a Firefox add-on, Zotero now also has a standalone desktop application, which can be used along with add-ons for Firefox, Chrome, and Safari. The browser extensions allow you to add references to your library with a single click, and if you have access to the PDF, Zotero will automatically download it to your library as well.

However, Zotero doesn’t come with its own PDF viewer, so you can’t annotate or highlight articles in your library. Instead, articles will open up with your default PDF viewer, which in my case is Foxit Reader.

Organizing your files is simple with Zotero as you can save searches of your library into subfolders. Any new items that fit the criteria will automatically be assigned to the subfolders as they are added to your library.

Zotero isn’t limited to only organizing PDFs, you can download and organize many different file types including images, audio files, and video files as well as snapshots of web pages.

Citations are also incredibly easy with Zotero, either through using the plug-ins for Microsoft Word or Open Office or through exporting the entire library into several formats including BibTeX. You can even add references to e-mails and other programs by simply dragging and dropping them from your Zotero library.

Zotero does support cloud syncing to its own servers, and with a free account, you automatically get 300 MB of storage space. You can upgrade your storage to several different options including 2 GB for a $20 annual fee or 25 GB for a $240 annual fee.

Syncing can be set to automatic, meaning changes appear in your online library not long after they occur, ensuring that your online account remains up-to-date. You aren’t limited to syncing only to Zotero, as you can also sync to WebDav enabled servers such as DropBox, Google Drive, and Box.

A downside to Zotero is the lack of ease in adding existing PDFs to your library. Zotero doesn’t have a feature that allows you to import whole folders. Instead, you can drag and drop highlighted PDFs directly into Zotero, which might take some time.

Another downside to importing PDFs already on your computer is that Zotero won’t automatically create an entry (with citation details) of any PDFs you add manually.

You can retrieve the metadata for PDFs relatively quickly in Zotero with a simple click, and can even highlight multiple PDFs to save time, but the process of importing is much more hands-on and time-consuming than for other reference managers.

This finishes out our series on reference managers. The series is by no means a complete list of reference managers. Nor did I provide an exhaustive list of features. My aim was to simply introduce several of the more popular reference managers and highlight their outstanding features as well as their limitations.

Hopefully, you now have enough information to help you select the one most suited to your needs.

For more tips on keeping track of the scientific literature, head over to the Bitesize Bio Managing the Scientific Literature Hub.

1 Comment

  1. Felipe on May 27, 2013 at 10:46 pm

    Two important features of Zotero: when using it from the browser, an icon appears in the address bar whenever it detects a reference in the page –PubMed, ScienceDirect, Google Books, etc.– you are viewing (book, article, movie, etc.). Simply clicking on it allows you to import it to your current library. If there are many items, a check box list shows up.
    The second one is that Zotero is not only free, it is open software.
    A warning: it is sometimes a bit clunky… but my main library contains 6891 items right now, so I supposse it comes with a price.

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