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I use Docear to get an overview of the notes taken in my PDFs and Mendeley for citations. In the Docear help they explain, that simply highlighting a section in Adobe Reader will not create a parseable annotation, but Adobe Acrobat will. A workaround for the Reader is to mark the text, copy it and then highlight it. Reader has an option for automatically ...


I use EndNote, with the marked up PDF saved into the record for citing as well as populating the 'research notes' field with quotes that I would use regularly from that text. (See below image for an example) The later versions of EndNote (I currently use X7) mean that the saved PDF is also searchable and so sometimes I've discovered useful sections by ...


I have a habit of taking all the notes, comments and highlights I have made on a book or a long document and reorganize them all in a mind map. The benefit of mind mapping include reorganizing based on visual cues, story line flow, and other hierarchical classifications. This way not only my notes are preserved but also the book or document's knowledge is ...


The Kindle software is fairly good for this. This is what I use. Then there's Mendeley http://www.mendeley.com/ Then there's Zotero https://www.zotero.org/ which may not be exactly what you want but may be.

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