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My PhD thesis consisted of two published papers and one submitted paper embedded in some additional framing. For completion of my PhD, I had to upload my thesis to the servers of our academic library, where it is now publicly available.

However, afterwards, the third paper from the thesis was rejected after peer review. I performed substantial changes and submitted the manuscript to another journal. They returned it back to me, stating that I exceeded by far the allowed index of similarity (40 % similarity with 35 % similarity of a single source). I spent $100 for a plagiarism check only to find out that the source from which I was accused to have copied a majority of my work, was my own publicly available thesis. As my thesis contains my third (unpublished) manuscript, it naturally has a high similarity with the version I was about to submit.

How can I solve this?

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    What field is this in? In my area, this would be completely outlandish behaviour from that journal. However, some fields have very messed-up notions of prior publications. – Arno Jul 2 '20 at 8:09
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    Assume ignorance before malice. Have you informed the reviewers of your investigation and provided details? – Paul Jul 2 '20 at 8:11
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    @Paul: I do not assume malice but our chairholder disencouraged me to resubmit my paper there even if the issues should be solved. I will, however, still inform the editor just in case some colleagues of mine plan to submit their work any time soon to the same journal. – offeltoffel Jul 2 '20 at 10:03
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    In my experience, plagiarism detection software generally doesn't bother worrying about things like that, as it is used to search for self-plagiarism as well. – jakebeal Jul 3 '20 at 20:42
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    Did you state on the title page that the paper is a re-worked version of part of your dissertation? – Jim Jul 3 '20 at 20:53
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Most publishers I know explicitly permit (pre)publication of papers as part of a thesis. For example the copyright policy of Elsevier (the publisher you used as a tag) states:

Authors can use their articles, in full or in part, for […] [i]nclusion in a thesis or dissertation (provided that this is not to be published commercially)

Going by this, everything is fine with your submission. More generally, you did not attempt to sell a work previously published in another journal (or parts thereof) as a new publication, which would be the typical case of self-plagiarism. For all of this, it does not matter whether you modified the respective chapter or included parts of the frame, as long as you stayed away from the already published chapters. However, the rejection of your paper may not have taken this into account, either because it was automatic or somebody did not connect the dots. I thus advise to consider the rejection to be an unintentional error or their side.

I would therefore simply write to the journal explaining that you suspect that your paper was mistakenly identified as plagiarism due to similarity with your thesis, which is fine as per the above rules. In general, it is a good idea to mention upon submission that parts of your paper have been previously published, be it as a preprint or thesis to avoid exactly this as well as potential clashes with journal policy.

Finally, to address some of your concerns:

I feel like [writing to the editor] may be conceived as begging for permission to be allowed into a reviewing process

I would not worry about this. First, what you are challenging is not a judgement call (e.g., a desk rejection due to lack of relevance). The journal stated a very objective argument for rejection (plagiarism) and you have very objective arguments that this argument is erroneous. It’s a simple mistake; it can happen; you are asking for it to be fixed. Furthermore, even if this should be considered begging, you have little to lose: Right now the journal considers you a plagiarist (which you might want to set straight even if you decide to submit to another journal).

The copyrights of Elsevier allow me to use articles published under their flag in my thesis. My case, however, is the other way round: I want to publish something that has been part of my thesis in very similar form. The thesis is published, but it contains a part that is not peer-reviewed and has not been published as an article.

Copyright transfer to journal exists because the journal’s business model is selling your paper and they want to have some exclusivity on this. For this, the order of events doesn’t matter. My point with linking these policies is to demonstrate that Elsevier is generally fine with papers that are available as a thesis.

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    Send them your so-called plagiarism report as well. Who knows, maybe they used the wrong report? – Anonymous Physicist Jul 2 '20 at 9:36
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    The copyrights of Elsevier allow me to use articles published under their flag in my thesis. My case, however, is the other way round: I want to publish something that has been part of my thesis in very similar form. The thesis is published, but it contains a part that is not peer-reviewed and has not been published as an article. – offeltoffel Jul 2 '20 at 10:08
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    @smcs: As opposed to plagiarism, self-plagiarism is not bad per se, but only when it is used to trick others into thinking that you did some new work when you actually recycled your old work. This is bad if you publish the same paper twice or use the same material to obtain two degrees (because those are expected to be independent). Nobody expect PhD theses to contain exclusive work – in fact this would be usually a bad thing as it would mean good work being obscured instead of being broadly visible to the research community. – Wrzlprmft Jul 2 '20 at 19:15
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    @offeltoffel: Actually, I don’t see any peculiarities in your framework thesis. Except for the name matches what is usually called sandwich thesis or cumulative thesis. Either way, it does not matter whether the alleged (self)-plagiarism is with the frame or an included paper or whether you modified that content or not: Your paper was rejected on false premises and a simple clarification mail should solve this. It might be that your modifying the chapter made the journal not look closer when it should have (so your plagiarism scores were actually too low), but that’s still not your fault. – Wrzlprmft Jul 3 '20 at 6:46
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    @smcs: Peer-reviewed papers as an academic currency work because you cannot (ethically) get two for the price of one. Part of the academic legitimisation of journals is based on providing the backbone for this system. The other half is disseminating research with copy-editing, typesetting, etc., which also provides the revenue for the journals, whether paid for by the authors or the viewers (whether that’s worth it, is another discussion). Previously published thesis undermine this model, but so do pre-prints, but not enough that libraries stop buying them (mostly, for now). – Wrzlprmft Jul 3 '20 at 12:20
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Find a better journal. A large portion of papers published in journals were previously published in dissertations. A competent editor would have checked to see if the similar document was your dissertation. This is a mistake, but an unreasonable one.

I have never seen a decision letter that involved an automated check of similarity. In good journals, plagiarism is determined by humans, not computers, though computers do assist.

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    I have my doubts that a publisher even bothers academic editors with something they determined to be blatant plagiarism. And except for false positives, this makes total sense. Of course there still would be some incompetency involved at the non-academic handling, but the actual journal is not to be blamed for this (except for their choice of publisher). – Wrzlprmft Jul 2 '20 at 9:02
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    @Wrzlprmft A simpler explanation would be that the academic editors do not exist. – Anonymous Physicist Jul 2 '20 at 9:07
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    The journal is considered (one of) the highest ranked and most esteemed journals in the field of my research. I would rather say that "worse journals" put more effort into winning authors for their issues, whereas the higher ranked do not want to waste time with presumable plagiarism. – offeltoffel Jul 2 '20 at 9:14
  • The decision letter stated that most (if not all) [sic] journals use this kind of software. I would find it strange if good journals were able to perform plagiarism detection on their own... – offeltoffel Jul 2 '20 at 9:15
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    That is disappointing. In that case, follow Wrzlprmft's suggestion, and hope that it doesn't become the formerly most esteemed journal. – Anonymous Physicist Jul 2 '20 at 9:35
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I've never heard of this happening. Since it was possible to do so, I imagine everyone who now writes a thesis or dissertation is required to upload it to the library. I had to turn in two copies of each (before the internet). And many if not most of us go on to publish it or parts of it So I don't know if it's something unique to your field or the journals you are submitting to. Technically, copying your own work is still considered plagiarism, and I'm not sure how library copies are viewed - since people are able to presumably download them I don't know if this is considered being published. I guess for some journals perhaps it is. First, make sure to look very carefully at all the submission information for the journal. It that's a policy it would be mentioned. If you don't find anything there, I would politely write to the editor explaining the situation and see what they say. Truthfully, I'd be surprised if they didn't the exact same thing with their own thesis or dissertation, though perhaps before the internet.

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  • Yes, it's commonly required to upload the thesis to the university library. However, it's usually possible to ask for a publication embargo, to keep it non-public for some period of time to handle e.g. the publication process and potential patent applications. – Anyon Jul 4 '20 at 15:52
  • @Anyon: It is possible to restrain the publication of the thesis but it will delay the conferment of the doctoral. Frankly, I would not want to wait until all content of my thesis is published although it is considered the most sincere way. But I agree that this is the only way if the journals do treat my thesis as a previous publication and thus accuse me of self-plagiarism – offeltoffel Jul 6 '20 at 9:37
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    @offeltoffel It's indeed unfortunate if an embargo leads to a delay in degree conferral at your institution. I don't think I would want to wait either in that situation. – Anyon Jul 6 '20 at 14:08

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