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I have a frequently-cited paper in a manuscript, and I want to refer to it as "Paper I" in the text, which I can do with \defcitealias in natbib. However, I want also the acronym "Paper I" to be shown in the list of references at the end of the paper, which is automatically generated by bibtex.

Note that although I could easily do this by modifying the bibtex entry for Paper I in the bibtex library, I am not inclined in doing so because the same bibtex library is used for different manuscripts, and I do not want the indication "Paper I" to appear in the references of all my manuscripts.

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You can use multiple bibliography databases. You'll need to prepare a "special" .bib file with a copy of the entry you want to modify (and a different citation label).

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