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I am wondering if it is legal to submit a work as fresh manuscript to a journal although we have already uploaded it somewhere else as a preprint?

Most of the journals/publishers require that the work at hand should not be submitted anywhere else. So I am wondering how the people who firstly put stuff as a preprint on the researchgate and ArXiv deal with this issue!

Cardinal
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The answer is simple: those same journals have an explicit exception for preprint servers.

Consider, for example, the Nature family of journals, whose current preprint policy says, in part:

Posting of preprints is not considered prior publication and will not jeopardize consideration at Nature Research journals. Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.

If you are wondering about a particular journal, the Sherpa/Romeo database is a good information source and often easier than searching the journal's own pages for the applicable policy.

jakebeal
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    Not all journals have such an exception, I believe. Check to be sure. – Buffy Sep 06 '20 at 18:15
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    The word "exception" sounds like it should be the rule not to allow for it. I don't think this conveys the right attitude, I think a word like "regulation for preprint servers" would be better :) In any case, in physics it is pretty much the rule that it is allowed. – user151413 Sep 07 '20 at 19:00