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Books as well as individual highlights can be tagged and then retrieved for review according to categories. All notes by a particular author can be viewed as well.
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All possible in Calibre if annotations are in a column, but I use KATE (Notepad++ in Windows is the same idea) and I have a KATE Session for each project. I get a list of sessions when I open KATE. Then the session has all the in use text files in tabs. I open the wordprocessor window beside it. Usually I remove an annotation file from the session when the edits are done, but my projects directory structure allows finding it easily to add it back. Some data is in spreadsheets and sometimes I take a text snapshot and have it in a text file in KATE.