PDFs and Reference Management Systems

PDFA two part post piggybacking on Phil’s printing post from last month.  The first part is a quick list of indispensible (and FREE) tools you simply must have if you work with PDFs on a regular basis, and I assume we all do.  One allows you to make PDFs from anything, and the other allows you to annotate any PDFs anywhere.  The second part of the post is an overview of a relatively new reference management system I’ve been using for about a year now called Zotero.  If you don’t know about it, you will soon.  Catch both parts below the jump.

Part 1: PDFCreator & PDF-XChange Viewer

PDFCreator is a free tool that allows you to creat a PDF from anything that has the ability to be printed.  And when I say anything, I mean eh-ne-thin-guh.  Word.  Excel.  Internet.  Paint.  Other PDFs.  By downloading the tool, you will install a ‘printer’ to your computer.  When you’re ready to make a PDF, go to the print menu and select the PDFCreator from the dropdown list of available printers.  Clicking Print will allow you to ‘print’ the selection into a PDF document.  You will be prompted to save your file to your harddrive.  Designate a place and a file name, click OK, and your PDF will be created.

PDF-XChange Viewer is another free tool that allows you to mark-up or annotate PDFs you have saved to your computer.  Clicking Free Download on the linked page will download a zip file which contains the install file.  The first time you want to annotate a PDF, right click on the file and select Open With:Choose Program.  You’ll probably have to browse to the folder containing the PDF-XChange Viewer the first time.  For all subsequent annotations, the PDF-XChange Viewer will be available by right clicking the PDF file and selecting Open With:PDF-XChange Viewer.

Once in the PDF-XChange Viewer, you have several options.  You can add text as a ‘Stick Note,’ or a text box.  Or you can select ‘Typewriter Tool and type directly on the page.  You can also highlight, underline, or strikethrough text.  Arrows, lines, and other shapes can also be added if needed.  You can create bookmarks in your PDF for later use, too, if you wish.  When you’re done, just save it and all the annotations are saved into the PDF.  Any PDF viewing program will open the PDF with the added annotations, including Adobe Reader.

Part 2: Zotero

This was the real reason for my post today.  The other programs are nice, but the talk about reading PDFs got me thinking about reference management software.  Trust me, you have a lot of options to manage your references.  Popular ones include EndNote and RefWorks.  EndNote is a for-pay stand alone software program that is very powerful with many attractive features.  But you have to buy the software.  RefWorks is a web-based reference management system that allows access to saved references from any computer.  But unless your campus has a site licence, it’s also for-pay.  Both systems are great, and I don’t begrudge anyone using them.

Zotero1Allow me to introduce Zotero, though, for your consideration.  Zotero is a FireFox add-on (so, yes, you’ll have to use FireFox… but why aren’t you using FireFox already?)  It is not a stand alone program.  The big draw to Zotero, for me, is the one-click reference – AND PDF – saving tool.  When your browser navigates to a page containing information you may need to cite later, Zotero recognizes the data and puts a button in FireFox’s address bar (see image).  Clicking on the button fires up Zotero and Zotero saves the full citation information to your Library.  For instance, you could browse to the abstract page for an ACS article pertinent to your research.  The article button would appear in the address bar, and you could click it.  Zotero would save the citation, including author(s), journal, volume, pages, abstract and url.

The library integrates within FireFox (see image, click for larger).  Note you can create a nested folder tree within your library, the papers in a selected folder display in the middle, and citation info appears on the right.  Along with citation information, you can add ‘notes’ to your reference.  If I’m just looking for a prep for one reaction, a typical note might read “Swern oxidation, cpd #13-14, Scheme 2, pg 2.   Prep on Supporting Info page S11.”  You can also ‘tag’ an article just like you would a blog post.  After you’ve collected several articles, you can quickly pull up all articles with the same tags.  I think some journal sites may automatically load their pre-determined tags on your behalf.


But the coolest part, imho, is the ability to attach files to your citations.  Including PDFs.  That means you can save the citation for your pertinent article – AND attach the full-text PDF (and supporting info, if necessary) to your citation.  The PDF attachment is saved to your local hard drive.  Meaning you can call up the full text PDF even when you’re not on campus and can’t use your campus journal subscription.  You can see the PDF I’ve attached in the image above.  AND in the preferences menu, you can have Zotero automatically attach PDFs to your citation for you.  AND you can click on the PDF in your library and select Show File to browse to the folder containing that PDF.  AND you can double click the PDF in your library to open the PDF in your browser.  AND if you’ve annotated your PDF with PDF-XChange Viewer, the annotations will show in your browser when you double click the PDF in your library.

Other cool features include: if you’ve searched, say, the ACS website and got a dozen or so hits from your search critera, the article button in the address bar is replaced with a folder button.  Clicking the folder button will allow you to grab the citations for several articles (AND their corresponding PDFs, if you have that option selected) all at once.  Also, Zotero will gather info for more than just journal articles.  Books, magazine articles, newspaper articles, podcasts, and many (many) more citation types can be stored and sorted in Zotero.

Now, I understand that you have a lot of inertia behind the reference management system you currently use.  I probably wouldn’t switch from Zotero now because I already have all my references stored there, and I’d have to go back and re-enter them all in something else, right?  Wrong.  If you use EndNote, you can export your library from EndNote (and others) and import it into Zotero in one easy motion.  You can also export from Zotero, if you end up not liking it.

Just like EndNote, you can use Zotero to create bibliographies in Word or OpenOffice.Org Writer.  See here.

I’m sure there are other cool features I don’t know about and don’t use.  If you’re a Zotero user, and you notice I’ve left out something, leave it in the comments.  For people who don’t use Zotero, definitely check out the quick start guide and the FAQ page.  Any questions, leave ’em in the comments and I’ll try to answer them.



  1. Zotero sounds interesting. I’ll have to wait until it comes out for Google Chrome.

  2. catching some ZZzzzzs says:

    AND in the preferences, if you turn on ‘PDF Indexing’, you can search the contents of the PDFs too. Can’t remember the author, but can remember the University? Just search on that, and Zotero will find the author’s address inside the PDF file.

  3. I would urge you to look at Mendeley too, it can automatically take data direct from saved PDF files, making the job very easy.

    It’s still in beta, with a few kinks, but these are being ironed out as we speak.

  4. Of course, the other way “to create a PDF from anything that has the ability to be printed” is to switch to a Mac. It’s built in, free, and just works. (You can still run windows in a fast intel-native emulator for legacy apps or if you swing that way…)

    • yeah, figured the Mac argument was coming 🙂 You can also use Papers for your reference management software. I don’t have a Mac, so I can do neither.

  5. You can also sync your zotero library for free on their server. It does not sync the PDFs (that requires a webdav server which is a cheap option if you need it). The nice thing is that you can use multiple computers and have your zotero library on all of them. You can also set-up a group library where the entire group and add references or create notes about ref. etc.

    • I was wondering if you could do that, or if you needed to store your library on a jumpdrive. Thanks for letting us know 🙂

  6. Joseph Peabody says:

    “One allows you to make PDFs from anything”

    m-m-m-m-macintosh system X?

    • My favorite example of the 3 operating systems:

      How do you add an accent mark over an e?

      Mac: option + e
      Windows: alt + 0233
      Linux: you’re on your own

      • Linux? At least in Ubuntu you can add a palette of accented characters to the menu bar. Ver’ ver’ useful.

        Well reminded about zotero! Have often narked about the lack of filing of pdfs and the disconnect between tham and reference management software.

  7. Allen Templeton says:

    I’m a big believer in PDF.

  8. Yup Zotero is indeed a great reference manager. The function I really love most is the ability that it can highlight and add comments in the PDFs. It is really a very useful feature for research.

    I do have one suggestion though. I feel that the ability to extract metadata can be improved. Very often, Zotero is unable to get the data or only gets part of it. This makes it hard to cite the articles. I tried uploading my articles into my colleagues wizfolio account (I believe it is another reference manager) and it was able to get the full information. Do hope that Zotero can improve in this.

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