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Thursday, December 3, 2015

Zotero – Finally a Good Reference Manager

If you are from my generation, you know what UP UP DOWN DOWN LEFT RIGHT LEFT RIGHT B A START means, your first e-mail account ended with hotmail.com, and the first five times you tried to use a reference manager, it sucked up so much time you were better off setting type by hand.

The fifth reference manager I tried, in October 2010, was Zotero. It wasn’t user friendly, had limited options, and I soon dismissed it like all the others.

But recently, thankfully, some people pointed my attention to Zotero again, and said it worked great. In first instance, I categorized them as people who will even say GitHub is user-friendly. You know, because they are tech-savvy youngsters who programmed in Minecraft on their iPad when they were 5.

But Zotero is great, and I’m so excited I just need to tell you some of it’s great features before you, like me, go on without it because you still think nothing can beat copy-pasting references by clicking Google Scholar’s ‘cite’ button.

Zotero has a standalone app. You can download it here, but be sure to also install the extension for the browser you use. If you load a webpage that has a scientific article on it, a symbol (either a folder, or a page) will appear in the browser bar. 
If you click it, Zotero will automatically add the reference to your database. If you thought that was cool, wait until you see that Zotero also automatically downloads the PDF file (if you have access to it). If you use it on Google Scholar, and there’s a link to a PDF file there, Zotero will also download the PDF file (see below).

That’s right. In one click, you have the reference, and the PDF file stored in your database. See the .gif below that illustrates this process.

Talking about the database: wouldn’t it be nice if the database could be synced across multiple computers? It surely would, and it surely can!

Set up a box account. It will give you 10 GB to sync (which should be enough) for free. The Zotero servers will only allow you to sync 300MB for free, which is enough for the database, but not for the attachments. Create the account, and use dav.box.com/dav and your account name and password to sync (see below). Wait for everything to sync (I had 3 GB, which took a while), and then you can download the files to a second PC.

If you already have a large number of PDF files on your computer, just drag them into Zotero, select them, right-click, and choose ‘Retrieve Meta-data for PDF’ (see the .gif below). Zotero will recognize most (but not all) PDF files. If you have a few thousand articles, Google Scholar (which it uses) will block you for a day. Be patient, and spread out the automatic recognition over a few days.

Obviously Zotero comes with an easy to use add-in for word, and adding references and the bibliography is really easy (in any citation style you want – it has APA 6th edition). After enabling PDF indexing in the options, you can use Zotero for a super fast search through the content of all PDF files in your database. You can also create groups – I created two, one for each PhD student I supervise, so I can easily share papers I come across with them when I think they should read them, and vice versa.

In short, I’m completely sold. I was missing out on a great tool. Thanks to Maarten Derxen and Mark Dingemanse for convincing me to try Zotero again. 

Are there some cool features of Zotero I missed? Let me know in the comments!


  1. I like that Zotero's open source nature and the community around it, allows you to extend it to do novel, unintended things.

    A small example: a consortium our research group is in, wanted a low-key way to share literature during the desk study phase.

    Accepting an invite to a Zotero group is a small effort, and you have an instant way to share your ongoing literature review.

    However, you need to keep it on participants mind somehow, so I wrote a small Python script that emails all participants a bi-weekly summary of articles added, and who added it. The overview uses the build-in citation formatter to generate nice references in the mail + a link to the full-text in the private Zotero-library.

    This is only possible because (1) Zotero is completely open, allowing third parties to develop things against their services, (2) there is a community releasing code to support that, (3) people don't have the feeling they are contributing to the bottom-line of some publishing dinosaur like Elsevier (Mendely) or Thomson Reuters (Endnote), with vested interest to channel scholary communication in certain directions.

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  3. You can use the extension Zotfile to handle pdfs in many ways, e.g. automatically rename them (e.g. to FirstAuthor-Year-Journal.pdf)

  4. I also really like ZotFile. For me the best feature after the automatic renaming is that it will put your pdfs in a folder structure defined on collections. So without a box account to sync across devices, I have my 'Zotero' folder in Google Drive, which I can access from anywhere, with subfolders and papers in them. If I would ever decide to stop using Zotero, I would still have my files stored in a searchable and organised way.

  5. As further proof that I'm not really a "tech-savvy youngster": I didn't even know that one can simply drag pdf's into the zotero window to have them added to the database. So thank *you*, Daniël.

  6. I'm very happy with Mendeley, that I recently switched to after horrible problems with Papers (not worth the money, in my opinion).

  7. Why is it better than Mendeley? Except the fact that it is not owned by Elsevier (which is worth a debate on his own)

    1. With Mendeley, you can sync only 2GB of files for free. That's not enough (my current library is 3.5 GB). With Zotero, you can very easily sync 10GB for free using Box. That alone makes all the difference for me at the moment, but people with more experience with Mendeley might be able to add other advanatages.

    2. Additionally, most people probably have access to DAV storage through their institutions.

  8. Quick installation instructions:


    Also, don't forget added benefit of off-campus proxy access to your favourite journals!


  9. I second Zotfile and would also like to mention Qnotero for quick access without having the standalone app open http://www.cogsci.nl/software/qnotero

  10. Great post. Thanks. Very happy with Zotero for a while now but learned new things.
    Only thing I'm missing is a smartphone app. Tried Zandy, but at least a few months ago it needed a lot of work.

    Anybody know of an alternative?

    1. I agree that having an app would be great - for phones or for tablets. The best solution for my Android phone so far is to use the ZotFile extension, which lets move files to a dedicated dropbox folder. If you then use an app such as DropSync, that folder will be automatically kept synchronised on your phone. After you make changes there, you can go to ZotFile and say "remove from tablet", and it will reconcile the two versions and all highlights/annotations...

    2. On iOS PaperShip is an excellent client app.