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I would like to cite a paper from a conference proceedings. The proceedings has been published as a special issue of a journal. Which is the best entry type, @article or @inproceeding, to use in this case?

@inproceeding allows to add data about the event; that I would like to inlcude, but then I don't where to put the journal name.

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Definitely @article. "Special issues" of journals are commonplace. Many journals let more than 50% of their issues be "special" in that sense. The main point of a bibliography is to aid your readers in locating the entries. Since you will always find the "special issues" of a journal together with the other issues of the journal (either physically in a library or online), you should list them as issues of that journal. If necessary, use the field issuetitle (or issuesubtitle/addendum/note) under @article to put in whatever the issue says about it being "special".

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@Inproceedings is the way to go. Is the journal name not (part of) the booktitle? Otherwise there's the series field, but it might not be passed to the document, depending on your bibliography style.

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