Where is that PDF???

April 22, 2010 at 3:13 pm 2 comments



You know you downloaded that PDF.  But where is it?  Guess what?  Now there are programs available to help you manage your PDF Collection.  

Mendeley is one you might be interested in.  For one, it’s free!  You can download the desktop application and/or access your PDFs via the Web.  It works on Windows, Apple and Linux operating systems, and you can use either Internet Explorer or Firefox to access it via the Web.  

Let’s say that you have all your PDFs stored in one folder on your hard drive (or your H:drive). You can configure the desktop application to pull all those PDFs into your Mendeley collection(s)– you can set up different collections within Mendeley.  Any time you add a PDF to that “watched” folder, Mendeley will automatically pull it into your collection.  Just a word of caution– Mendeley doesn’t distinguish the content of PDFs — it pulls in all the PDFs and you may discover, as I did, that your PDF Dental/Vision Form gets pulled into Mendeley!  Once the PDF is in your Mendeley collection, you can annotate and highlight sections of the PDF.  You can add tags and notes to the reference to easily find all records that have certain tags or notes.  

Mendeley desktop application

Mendeley desktop application


If you don’t have administrative privileges on your work computer to install the desktop application, download it to your personal computer, and then use the web-based application.  You can sync your collections between the desktop application and the Web.  One caveat is that you can only store up to 500MB on the web server.  However, Mendeley will be offering a premium package to accommodate those requiring more storage space.  

Mendeley Web

A record in Mendeley Web


You can use the web importer to import references from PubMed, Google Scholar, EBSCO, ISI Web of Knowledge, Ovid SP and many more.  However, importing the references from these databases does not import the PDF.  But, if you have access to the PDF, you can download it, and then drag and drop it into the reference.  

If you have EndNote libraries (or BibTex, RIS, or Zotero) already set up, you can import those references into a Mendeley collection.  And, if you’re using CiteULike, you can synchronize between the two to import documents from CiteULike into Mendeley.  (Check out Mendeley’s FAQ for these instructions.)  

Once you’ve set up in Mendeley collections you can share them with colleagues. Mendeley can also be used to format bibliographies in a manuscript for publication — much like you do with EndNote.  There are over 1000 bibliographic styles.  

For more information, visit the Mendeley Web site; they’ve got a forum set up where you can ask questions, make suggestions for improvements and vote on suggestions that have already been submitted.  

View the screencast for a quick overview of Mendeley (5 minutes in length):

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  • 1. Vitaly Herasevcih  |  May 21, 2010 at 10:01 am

    There are problem with import-export between EndNote and Mendeley. Not 100% of fields can transferred. It will be improved in future.

  • 2. Dr. Gunn  |  May 22, 2010 at 11:12 am

    Thanks for the nice article.

    If anyone has issues with importing Endnote files, please email support@mendeley.com, but before doing so you might want to check that you’ve exported from Endnote in XML format not RIS format, as the import works much better with the XML files.

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