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I usually read my books using an application called Mantano on Android. They have a cloud based sync mechanism that syncs annotations across various mobile devices.

My problem is I want to keep all my books in Dropbox (or maybe Calibre) and want to keep all the annotations, bookmarks in one place (preferably within the book itself) so that if in future I want to change the reading software on any platform, I have the annotations right there.

Is there any solution for this? I mainly read epub and pdf books. A single reader is the best option but if not possible I can use two readers (one for pdf and another for epub). I want to stay away from dedicated readers like kindle, nook etc.

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  • That would require to keep the annotations etc. inside the book file itself -- which is theoretically possible for PDF and EPUB3 (though only supported by few apps this way). I don't know any app handling it this way for EPUB. For PDF, it seems like ezPDF Reader Multimedia PDF in its paid version is capable of this -- I did not try it myself, but got PDFs edited this way (maybe @ce4 can clarify?).
    – Izzy ♦
    Jan 26, 2013 at 19:05

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Two options:

  • backup Mantano's database (or the whole mantano folder)
  • use Adobe Digital Editions to extract the annotations

The first option will keep you locked in Mantano. The second in ADE, which more applications use it, but it's not as pervasive as one would like. The main problem with .epub is that annotations aren't part of the standard, thus every application that supports it has to implement annotations in their own way, which usually means storing them out of the file.

For PDFs, I use Repligo, which stores the annotations inside the PDF. But many others like ezPDF accomplish this.

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