Mendeley is a powerful reference manager that’s free to use, and does a great job of sorting and organizing papers complete with highlights and annotations. That said, its features are still sometimes limited, with bugs that continually need to be ironed out. Here I’ll explain how I use Mendeley to organize my scientific articles in a somewhat convoluted, but effective way.
What you’ll need:
- Mendeley Desktop
- Adobe Acrobat/PDF XChange (some PDF reader/editor)
- Dropbox/Box.net (a cloud service)
- Mobile version of Mendeley (Mendeley on iOS, Droideley or Scholarley on Android)
- Mobile PDF reader (I use Repligo Reader)
Cloud-based storage
Create an account for yourself on Dropbox, Box, or any other cloud storage that has a desktop sync option. This will let you have access to your journal articles anywhere without having to carry your computer or laptop around. Size requirements depend on how many articles you have, I use Box for my articles, as they have a free 25GB account offer.
Mendeley Desktop
Here’s where the bulk of your work goes. First, have Mendeley organize your library for you. You can do this by going to Tools > Options > File Organizer and check the “Organize my files” option. Have Mendeley copy your files to a folder that you set up within your cloud account (for example: C:\Users\Your Name\Documents\My Box Files\Mendeley). Arrange the remaining options however you would like.
Then, import all your journal articles. Assuming you’ve set up the cloud folder, Mendeley will copy and sort each article into its own filing system. Once this is done, you are free to delete the original file. Note that some files will be hard for Mendeley to read, and they may not extract the right information (Title, Author, etc). In these cases, Mendeley will alert you by tagging them “Needs Review.” When you have fixed these articles, Mendeley will sort them as appropriate.
Reading articles
While Mendeley has native highlighting and annotation tools, these highlights are only kept within the Mendeley database, and not on the PDF file itself. To get around this, I make all my annotations in a PDF software with editing capabilities, such as Adobe Acrobat Reader or PDFXChange Viewer. To open a article for the first time, right click and select “Open File Externally.” Then in your default PDF reader, make all the highlights and annotations, saving after you have finished. Your annotations and highlights will now be synced in the cloud, allowing you to read your notes wherever you are.
Mobile access
Mendeley can be accessed on tablets or phones using any of the apps I listed above. Each has their own strengths and weaknesses, play around with them to find your favorite.
If you want to edit your annotations or add highlights on the go, you’ll need a mobile PDF app. I use Repligo Reader. Just use your Mendeley app to retrieve the PDF or use your cloud storage app (both Dropbox and Box offer very nice mobile apps) and you can edit away to your heart’s content.
That’s it! You now have a journal library that you can read all your papers on the computer with, complete with note-taking and highlighting. And it’s synced to the cloud, allowing you to access all your notes wherever you want.
Jay says
June 21, 2016 at 12:24 pmHello,
I was wondering if this solution syncs the annotations and notes as well? Or is this solution only for the PDF documents?
George Chen says
June 21, 2016 at 12:39 pmWhat I do is put my notes and annotations into the PDF using Acrobat or Preview, that will preserve the notes for sure. I’m not sure if doing it through Mendeley will – a few versions ago, I realized that Mendeley’s highlights were internal and not preserved on the PDF file (if you opened the PDF outside of Mendeley it would be blank). I don’t know if that’s changed with the most recent version.
Jenn D. says
January 2, 2015 at 10:32 amOk, thanks for the clarification!
In case it’s helpful, here’s what I found …
When you click mendeley’s web importer plugin it saves the metadata primarily and only the pdf if you want it to (based on what I read, this might be new functionality — not sure since I’m a new user). Anyway, in the case of an arxiv paper, when clicking the mendeley plugin to save it, you can un-click the “save the pdf” option (and also avoid clicking “open in mendeley” after metadata is saved) in order to not store-to-disk freely available stuff. This way mendeley just keeps it as a link to arxiv. For papers behind a paywall or login the following seems to work for me.
1. go to paper at journal’s website
2. click the mendeley plugin to save metadata entry to mendeley
3. obtain paper via institutional login and then move the paper to box.com account or other cloud service
4. open up mendeley and edit the paper entry’s url to point to my box.com share link for the file instead of pointing to the journal page.
It’s a bit of excessive clicking around, but for me it may be worth it since I have come to use my travel computer as primary.
George Chen says
January 2, 2015 at 3:11 pmThanks for that, I think that may be the best workaround so far.
Jenn D. says
January 1, 2015 at 12:37 amHi,
Thanks for the post. You say “This will let you have access to your journal articles anywhere without having to carry your entire collection around” and then in the next section you say “Have Mendeley copy your files to a folder that you set up within your cloud account (for example: C:\Users\Your Name\Documents\My Box Files\Mendeley)”. Since this path is on one’s computer, can you help me to understand why these two statements don’t contradict? I would like to have the files on the cloud without having to sync and carry around the files on my computer. Let me know if you know of a way to do this and thanks in advance !
George Chen says
January 1, 2015 at 6:30 pmAh! My mistake. I meant to say “without having to carry your laptop or computer around.” You’re right, will fix that in the post. As of right now, I’m pretty sure Mendeley doesn’t have the option of just syncing articles to a cloud service without linking to a local file.
amir says
August 28, 2014 at 1:21 pmThanks for the brief help. here is a quesion how can i tell mendeley to not sync the pdfs into its server. I ran out of space and now it wants to charge me for cloud. i would be fine with my harddrive or dropbox being the cloud/server for mendeley. in otherwords i dont want to pay for multiple clouds.
Also, did you have any probelm when you are extracting info from web say ieee, with mendeley? and what is the best practice for those bugs?
Thanks,
Amir
George Chen says
August 28, 2014 at 2:21 pmTo stop the PDFs from Syncing with the server, you should be able to go to “Edit Settings” and turn off Sync. This will only sync the references to the Mendeley servers. On the Mac version, it’s the button right next to the All Documents header. I think it’s the same on Windows.
For websites, it’s a bit tricky. I tend to resort to manually creating an entry (File > Add entry manually). I may create a PDF of the page and add that as an attachment to the entry.
Hope this helps!