Reading inside Mendeley, better to avoid it

I have already started writing about the great research tool, Mendeley Desktop. I believe, mendeley is one of the mandatory tools every academician need to have. Many people are using it for many things. As to me, however, its main virtue is the ability to organize the actual PDF files in a brilliant manner. In this post, though, I am going to tell you why you need to avoid reading and annotating PDF files inside Mendeley itself.

If you are familiar with the fast and efficient PDF readers as Foxit and PDF-exchange, you will face too many constraints with Mendeley’s internal PDF reader, which I found to be unbearable. Of course, you can read, annotate and write notes inside mendeley. But, the main downside of Mendeley’s internal PDF reader is the fact that your annotations will be saved in separate folder. Mendeley has a system called database where it saves information about the PDF files. That database is in a different folder from the actual PDF files. Hence, if you open your Mendeley annotated PDF files in another PDF reader, you will not get the annotations. This is bad. I want my PDFs annotated wherever I open them, whenever I want.

Mendeley team has tried to alleviate the problem by adding a feature to export the annotations of the PDFs. But, I found this to be a laborious task. Should I open and export the annotations of each and every file every time I want to see my annotations in another software? no, I will not do it. So, if you are like me, the best approach is to manage your files inside Mendeley and read them using more potent PDf readers as Foxit. Your annotations and notes will be saved embedded inside the PDF files that you don’t have to worry opening them in another software.  You will enjoy your annotations to the  end of time (unless you want to remove them of course) wherever you go, which ever software you use.  So, to  open the files organized inside Mendeley with external readers, you have to right clicking the file and choose “Open file externally”. Your default reader will be fired. Voila!



Update: 2017-07-19

I don’t know that people still check  out this post. I wrote this in 2012.  I want to update  my latest experiences. I have given up with mendeley. I am now encouraging people to move away from this applicattion because the reference data it downloads is complete junk. The user has no option to download data from Woldcat or some other better source (national or international libraries; publishers like Jstor etc). I am now using am amazing reference manager called Bookends. Since I moved to Bookends, I am able to maintain a bigger, and clearer reference data.

Zotero is also a great tool.  For the peopl who use Latex, Jabref recently has grown extremely powerful reference manager. It has gone a lot of transformations. I highly encourage you to check out Jabref. Other great tool in the Windows is an application called Qiqqa. Citavi is also ok.  You can check out this post on the comparison of the other reference mangers.


13 thoughts on “Reading inside Mendeley, better to avoid it

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  1. Thanks for using Mendeley, dellu! You’re correct that annotations are stored separately from the PDF file itself. The reason we do this is so that you and your colleagues can all collaboratively annotate and share papers. You may wish to have one set of annotations on a PDF which you’d like to keep private and another set of annotations you’d like to share with the members of the Mendeley groups into which you place the PDFs. If we wrote the annotations into the file, not only would it be challenging to keep your annotations and those of others apart, but it would risk exposing your private annotatations when you share a PDFs.

    Thanks for the feedback and we’ll continue to work on improving both the standalone and the collaborative means of PDF anotation.

    1. sure, I now understand why you guys decide to keep the annotations in a separate file. Mendeley has the collaborative spirit in it and there the privacy question kicks in. Got it! Thanks for the explanation and for checking out my page. It is my pleasure to hear from the Mendeley team. I will be writing more about Mendeley’s great features in the future because I love the application.

  2. I’m moving my files to another computer. Then, where are comments, highlights and annotations saved in Mendeley? and how I can import/read them?

  3. I’m sorry Mendeley but comments need to live with the document. As in standard pdf comments. And they need to be searchable. Dellu is right.

    Collaborative documents is over hyped. Academics are individual creatures and prefer to keep their notes and if you had private stuff who would trust any software?

    Mendley still searches only notes, not comments, rendering it useless for effective document management.

  4. Hi, I understand the reason that Mendeley saves annotations separately from the pdf. But there is another pressing problem keeping me from directly annotating in Mendeley – it’s utterly clumsy and limited mechanisms for highlighting, adding comments/notes as compared to Foxit reader and PDF-exchange.

  5. i think if the private annotations were searchable, Mendeley would gain so much.. I don’t understable why it is not possible to search in the private annotations.

  6. My other trouble is when I have annotated a file elsewhere, there isn’t a way to import those to Mendeley. I have 100s of files I’ve been gathering for awhile, but when trying to import them to Mendeley, the notes aren’t included. I can’t figure out how to do that, either.

    1. Is it any good? Specifically, if it’s compatible with Adobe annotations and if it’s any kind of modern when it comes to orienting in the document (zooming in by pinching the notebook touchpad – can’t believe so many readers still don’t have that feature today)

      1. Yes, Foxit is good reader. The annotations are also Adobe standard. But, from my experience in the past, PDF-xchange was much better system overall.

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