In the eighth entry to our How-to series, we look at the built-in PDF viewer within Mendeley Desktop.
We (and many others) think that Mendeley is a great tool to organize your research documents. It’s also a great application to allow you to read, annotate and highlight your PDFs too! The built-in PDF viewer allows multiple open documents, highlighting, post-it-like note taking and more.
If you double-click an entry for which you have the PDF document available, you will then be able to view the document in the built-in PDF reader. You can have multiple PDFs open simultaneously, each in their own tab. Like most PDF viewers, you have the general tools that allow you to pan, zoom, read in full screen, etc. You can also annotate these documents. Highlight by selection, or by adding boxes. Add post-it-like notes in localized sections of the article and even leave article wide notes in the box in the right-hand panel.

You can see the PDF viewer in action 40 seconds into the following video:

There is something that must be made apparent here: your annotations are being stored in the given context in which they are added. This means that you can have a paper in your personal library with notes and highlights, and have the same document in a shared group with a different set of annotations and highlights. This is quite useful for many reasons, such as keeping personal notes privates while allowing you to share references and PDFs in private groups, maintaining your notes separate from group notes, etc. If you actually open the PDF file in an external PDF viewer, you’ll also notice that it has no annotations at all. This is because we keep annotations stored separately from the PDF, per se. Allowing you to sync your document across devices and also the annotations but keeping them in separate “layers”.

Now you may ask: How do I get my PDF with the annotations so that I can send them to someone who doesn’t use Mendeley? Or how do I print my PDF with annotations?
There is a solution for that, you can simply export the document with annotations or even better, just export the annotations (notes) to a PDF file.

Here’s how that is done:

1. Within Mendeley Desktop, double-click on a reference to open the PDF in a new tab for viewing.
2. Go to File menu and then select Export PDF with Annotations
3. A pop-up window will prompt you to select if you’d like to export the PDF contents with the notes and highlights, or just the notes.
4. Once you’ve made your choice, click OK and select the location and name you’d like to save the file.

There you go, you have an exported PDF with annotations and notes. These notes are now part of the file and can generally be reviewed in any PDF reader. Sadly, there is not yet a standard format for PDF highlights and annotation, so these may render a bit differently from PDF viewer to viewer.

Here are the previous seven entries in our How-to series:

• How to merge author names
• How to drag and drop PDF links into Mendeley for direct download
• Generate BibTeX files for your collections for use in LaTeX
• How to check for duplicate entries and merging
• How to copy & paste formatted citations anywhere (LaTeX too!)
• How to add supplementary data to references
• How to keep references and documents unpublished (out of catalog)