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I am doing some research and I do put lots of notes and bookmarks in the books (PDF files).

I am looking for a tools that will allow me to see and search inside all these notes.

I supposed that this tools should be able to scan a directory with PDF files, for notes and keep them in sync.

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I try to build a comparison matrix at spreadsheets.google.com/spreadsheet/… –  sorin Jul 4 '11 at 21:05
    
Your column for BibDesk is mostly wrong. Try using BibDesk + Skim. It lets you organize, search, and see notes. –  user588 Jul 5 '11 at 17:03
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3 Answers

Sounds like you need Papers

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Sorry, but Papers is not able to recognize standard annotations/notes made with Preview or Adobe Reader. They recognize only their own annotations. –  sorin Jul 4 '11 at 22:35
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What about Evernote.. There may be issues like limited uploaded. But you may go for premium option.

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You should try Mendelely, a Reference Manager with Dropbox-like sharing/syncing. It reads Comments from PDFs, but sometimes mixes them up. In my example i had saved an Article as a PDF with the Headline as the Filename, but Mendeley indexed my Comment as the Filename.

You should also take a look at Eaglefiler, as the name says more Archiv-oriented.

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