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I am using Mendeley to organize, highlight and to synchronize my references. I think a feature where you can see a list of annotations/highlight that you have made will be extremely useful during writing.

For example one day you just remember, "Oh I have seen this in some papers, I don't remember which one but I remember I highlighted it."

Right now I have to guess and open one by one the paper to look for the annotations that I meant and scrolling the screen to look for "it", or by performing a search, both are not efficient enough.

Kindle has this feature. Everytime you make some annotations (on different books) they aggregate and put it as a list for you. When you click on that, it will go to the page on the book.

Is there any reference manager that has this kind of functionality?

  • Mendeley is great and free, but If you are willing to pay the price I would suggest Papers, which I use in my Mac and iPad (and is also available for windows). It supports papers annotations (and synchronization). – ddiez Sep 15 '14 at 2:47
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Qiqqa will do this. Zotero will also do it, with the Zotfile extension (which can extract annotations from a PDF into a note).

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Another option is Docear, in which you organize your references in a mind map. It automatically imports annotations from your pdf files and puts them in the mindmap.

Like so

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Citavi does this (and I work for them).

You can simply highlight your PDFs, but you can also extract quotations and add summaries and comments. Quotations, summaries, and comments can be tagged and moved into the order in which you might want to use them for your paper, but they remain linked to the exact position in the PDF.

The video "Citavi 5 in a nutshell" explains how it all fits together: https://www.youtube.com/watch?v=X3vbWIcljDQ

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