I'm mostly using Mendeley, but after reading lots of ebooks with the Kindle app, I've noticed that I really like the feature that shows me the content of all highlights and the ability to jump to the relevant section. Is there any software for reference/paper organization, reading and note taking like Mendeley which has this feature?

As an example, for those who don't know this feature from e.g. Kindle, if the text above was part of a paper and the bold part was my highlight, I want to have a list that shows:

  • I really like the feature that shows me the content of all highlights
  • the ability to jump to the relevant section

and clicking on one of them should bring me to the respective section of the paper.

Any pointer much appreciated!

  • Zotero with the Zotfile addon will do this. It's slightly rough around the edges, but it works.
    – Flyto
    Jan 16, 2018 at 13:56

2 Answers 2


Citavi has the mentioned functionality.

There are (at least?) four types of highlighting: Direct quotation (what you are describing - in blue), indirect quotation (pink), summary (green) and comment (not shown, same as in standard PDF viewers). All of them can navigate to their original location when clicking on the link-icon:

Citavi quotes

I downloaded one of the apparently most popular papers of 2017 and marked three random parts. The titles copy (part of) your marked text per default, but you can change it if you want.

I think it's free for up to 100 references. But if your school has some sort of partnership program, you might be able to get a full license.

I switched from Mendeley to Citavi a few years ago. It was a little confusing at the beginning as I was expecting it to be "like Mendeley, but better", so I even used both parallel for some time. There are still a lot of functions I have no idea about, but documentation seems very thorough. At my school, there are even courses on how to use it.

  • Thank you very much! Unfortunately, my university seems to be one of the view that do not have a license. Purchasing my own for professional use would be 280 CHF. Private use is 149 CHF. Prices in Dollar are probably similar (1 CHF ~ 1USD). Tempted to try the free version, but afraid I will like it too much. Its a steep price... Jan 12, 2018 at 11:17
  • Also, Citavi for Mac is still in Beta and from a glance at their user forumit's still very buggy: support.citavi.com/forum/viewforum.php?f=16 Jan 12, 2018 at 11:49
  • I completely agree, it's quite expensive. Even for students it's still 120€, which just for the commenting function is probably not worth it. Have you checked Zotero? It's free, but I'm not sure if it has exactly the functionality you want.
    – fukiburi
    Jan 12, 2018 at 16:34
  • I havent but apart from that feature Im OK with Mendeley for now. A work around is to copy all commented (gets marked too then) and paste the text into comment with e.g. quotation marks. Thanks again for the recommendation! I will definitely give it a try, since I'm soon moving away from the Mac anyway. Jan 14, 2018 at 6:56
  • Im not marking your answer as 'solved' yet, since Im still hoping for more recommendations, but I will eventually. You can ping me if I forget about it. Jan 14, 2018 at 6:58

Zotero, combined with the addon Zotfile, will do this. Both are free and open source, which has the significant advantage that you know your extensive reference list, compiled over many years, will not suddenly be held to ransom where you must pay a subscription!

Screenshot of Zotero

In the screenshot, the PDF annotations (highlights and notes) are extracted by right-clicking on the PDF and selecting "extract annotations". Those annotations have the underlined link after each of them - clicking that will open the PDF at the right place.

It's a little rough around the edges at times, but it works well.

  • Thanks a lot. This does indeed look like what I want. Unfortunately it seems like storage for online sync is quite limited and I would have to pay for that, while Mendeley it is free at my Uni... Oh well. Jan 17, 2018 at 16:37
  • Aye - Mendeley is funded by a giant publishing corporation, while Zotero actually has to cover its own costs 😉
    – Flyto
    Jan 17, 2018 at 16:49
  • Sure. Is there any advantage of using their cloud function over having a shared folder (e.g. Dropbox) with the pdfs and bibtex file in it? Feb 21, 2018 at 13:47
  • @user1323995 only that if you use Dropbox and then accidentally open it from two computers at once, well, I don't know what would happen. I suspect it would have the potential to be Bad. You don't have to use Zotero's storage - it'll happily sync using any WebDAV space, if you have access to any. Google throws up whoishostingthis.com/compare/webdav. I've never looked into what this would cost, as I can afford $20-60/year and like to support them. YMMV.
    – Flyto
    Feb 21, 2018 at 14:15

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