Tuesday 9 June 2009

From zero to Zotero - One man's journey out of PDF hell

Zotero is a reference management software. Sorry, let me correct that - Zotero is THE reference management software. I had tried Zotero before, and it certainly looked good; but frankly I couldn't figure out how to get it to work and so reverted to my usual system, the 'zero' of the title. Hearing the news that Endnote vs. Zotero was just thrown out of court, I decided to try it again.

And it's just amazing.

Let me begin by describing a typical workflow:
(1) Go to the summary page for an ACS paper online
(2) Click on the icon that appears in the address bar (looks like a sheet of paper with writing).

That's it. You've just saved the PDF, the HTML full-text and the paper's metadata.

If you've created an account on zotero.org (free of course!), you can synch your library so that multiple computers can share the same data. And best of all you can also synch the attachments (i.e. PDFs, HTML pages) if you have a WebDAV account (e.g. from your university or in my case, JungleDisk Plus/Amazon S3). If that wasn't enough, it also integrates with Word to make it easy to prepare a publication (though I haven't tested this Update: it works just fine, but you first need to install the bibliographic styles you need from Zotero settings/Preferences/Styles/Get additional styles).

In other words, Zotero makes it easy to download papers, back them up, make them accessible from any computer and reference them in papers.

Zotero is open source and freely available from www.zotero.org.

Notes: I'm using Zotero 2.0b5. In the Zotero preferences (click on the gear icon), choose "Automatically attach PDFs and other files when saving items" in the General Tab. JungleDisk and Amazon cost money (we're talking around $1.50 a month), but there may be free alternatives for WebDAV. For any websites that aren't currently supported by Zotero, adding new translators has been made easy. All of the JavaScript files for the translators are stored in a folder on your computer and can easily be extended or added to. That said, I've had no trouble downloading PDFs from Sciencedirect, ACS, RSC, Wiley or BMC.

Image credit: jazzmodeus


greg landrum said...

It also integrates reasonably well with OpenOffice, at least on some platforms.

As an added bonus, you can tag papers and add (searchable) notes; no more "should I put this PDF in the VirtualScreening or Similarity directory?" hell.

zotero really is excellent.

TheDoogs said...

wow. I didn't even know this existed. Just tinkering for 15 minutes so far and this really is amazing... thanks

Robert W. Gehl said...

Yes, and you can also do timelines with Zotero really easily - something I do all the time. You can see what it looks like on my blog: http://robertgehl.blogspot.com/2009/06/another-reason-to-love-zotero-timelines.html.

So when you gather sources (PDFs or otherwise) you can put them into timeline form to make your work a bit more visual. It's a big help for me.

Anonymous said...

Hey - the most amazing way to go from Zero to References is this new feature in Zotero:
(just watch the little movie).

Somehow it takes your pile of random PDFs, and magically identifies them and puts all the information there for you! I couldn't believe my eyes the first time! This has allowed me to go from literally thousands of PDFs stored all over the place to a beautifully organised and tagged database with all the bibliographic info in less than a day.