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I currently use org-ref and helm-bibtex with one notes file per source to manage my library. For any given source, I may have several headers, each for notes on different chapters or topics I have captured.

But now I want to cite a note, and I want to include the page numbers it references...

But how do you do this with only one notes file per source? And if notes get broken out into individual files, each with their own citation, how do you avoid having multiple citations for each source show up in my helm-bibtex search window, each with the same title and author, etc?

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In org-ref, you can only cite a bibtex entry, and not a note. You can annotate the cite link with page numbers e.g. [[cite:some-key][p200]], and that annotation is done manually.

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