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Let us suppose one publishes an article in a peer-reviewed journal that is archived, indexed, etc. in databases such as Zentralblatt, ResearchBib, etc. Does the author have to manually submit his/her information and his/her journal article to those databases, or this is done automatically by the journal or by such databases?

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For Zentralblatt or MathSciNet, which are by far the most important databases in mathematics, there's no need to manually submit anything. I would assume the same is true for any comprehensive database (if you depend on author submissions, you won't get anywhere near complete coverage), but I suppose it could depend on the particular case. I've never heard of ResearchBib, so I can't say anything there.

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