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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 As my thesis contains my third (unpublished) manuscript, it naturally has a high similarity with the version I was about to submit.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?

Wrzlprmft
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offeltoffel
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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 02 '20 at 08:09
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    Assume ignorance before malice. Have you informed the reviewers of your investigation and provided details? – Paul Jul 02 '20 at 08:11
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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 02 '20 at 10:03
  • Are you saying that papers with a lot of similar content should be accepted simply because of who wrote them (namely the same person)? – Kaz Jul 03 '20 at 20:48
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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 03 '20 at 20:53
  • Did you try emailing the editor explaining the situation? Namely, that your on-line but not refereed thesis fragment is generating the (false) positive? – paul garrett Jul 03 '20 at 22:07
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    @Kaz: no, they're saying (rightly or wrongly) that the fact their thesis is in some sense "published" should not imply that it's somehow bad for the same material also to appear in a journal. And indeed the publisher broadly agrees with that position, even if this editor doesn't. There aren't two similar "papers" unless the thesis is a "paper". – Steve Jessop Jul 04 '20 at 03:31
  • Did you do something daft, like using a different spelling of your name or leaving out a middle initial? I'd sort of expect the software to notice if the author's name was the same. How many John Smiths can there possibly be? – Bloke Down The Pub Jul 03 '20 at 20:26
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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 03 '20 at 20:42
  • Am I getting this right? The article was basically accepted, and the reviewers now worked for nothing just because you don´t want to write the editor to straighten out a mistake (likely yours, not citing your dissertation, and not writing in the accompanying letter that this is 1/3 of your recently finished thesis? Because you´re huffy over your waste of 100$? – Karl Jul 04 '20 at 09:31
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    @Karl: From what do you deduce this? The journal that peer-reviewed it rejected it regularly after peer review. The asker then made changes and submitted it to another journal, which desk-rejected it due to (self)plagiarism. Also, please be nice. – Wrzlprmft Jul 04 '20 at 09:43
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    @Karl, I think Wrzlprmft wasn't clear enough, so I'll say it: No, you're not getting this right at all. Everything you said was wrong, and came off as quite rude. – Mike Jul 04 '20 at 11:59
  • Publishing your thesis is fine (and I've done it), the paper should just cite the thesis properly as @Jim suggested. – Blaisorblade Jul 05 '20 at 09:16
  • I understand that the matter is complicated. Wrzprmft summed up the situation correctly. As for what @Jim asks, I'll have to admit that in the cover letter I did not mention that the study had been submitted to another journal (and rejected after peer-review), because it underwent substantial changes and I only kept the wording for the introduction and some little parts of the discussion. Nor did I mention that the rejected form of the manuscript is publicly available in my thesis. It is, in fact, a different paper but with high similarity. – offeltoffel Jul 06 '20 at 09:42
  • https://academia.stackexchange.com/questions/2937/can-i-publish-parts-of-the-ph-d-thesis-as-a-paper-in-a-journal – Anonymous Physicist Sep 02 '21 at 12:45

3 Answers3

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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.

Wrzlprmft
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    Send them your so-called plagiarism report as well. Who knows, maybe they used the wrong report? – Anonymous Physicist Jul 02 '20 at 09:36
  • Thank you for this link! I know for a fact that they used the exact same software for plagiarism detection and I obtained the exact same similarity-index which leads me to believe that the check was fine but the conclusion was not. I think I will write to the editor, even if I feel like this may be conceived as begging for permission to be allowed into a reviewing process – offeltoffel Jul 02 '20 at 10:01
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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 02 '20 at 10:08
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    @offeltoffel: Please see my edit. – Wrzlprmft Jul 02 '20 at 10:27
  • Thank you for caring to explain your thoughts in such detail. I have asked the journal to inform the editor-in-chief to contact me and I will try to make my point there as well! I will keep you updated on the situation! – offeltoffel Jul 02 '20 at 12:05
  • I'm inexperienced.. assuming that at least parts of the text appear word for word in both publications--why would this not be considered self-plagiarism? – smcs Jul 02 '20 at 17:04
  • @smcs: the frame thesis consists of a copy of my three publications and additional text "framing" the articles. The third "publication", however, never got published. It was still under review at that time and let down later. I "recycled" lots of this stuff, though, for a proper new publication – offeltoffel Jul 02 '20 at 17:14
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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 02 '20 at 19:15
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    @Wrzlprmft Your last comment makes a very good point since many people are confused about self-plagiarism. I wonder if it should be mentioned in the answer. – Luca Citi Jul 02 '20 at 19:51
  • @Wrzlprmft: I agree with all your points, but still I think I need to emphasize something: the presumable self-plagiarism did not concern the actual "framework chapters", but the chapters with the 1:1 copies of my three publications. Only that one publication actually never got published (which I am trying to make good for with my new submission). But I see how the journal could think that it has. The concept of a framework thesis seems to be different around the globe, that's why I am stressing this point. – offeltoffel Jul 03 '20 at 06:25
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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 03 '20 at 06:46
  • @Wrzlprmft Thanks. I understand that a PhD thesis does not have to contain exclusive work, but a publication in a journal has to, right? From the standpoint of the journal, why does it matter whether I sent them copy & pasted parts from a previously published paper or a previously published PhD thesis? – smcs Jul 03 '20 at 11:54
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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 03 '20 at 12:20
  • In case you are interested in an update of the situation: the editor has responded that "[if the similarity occured from [my] thesis, it may not count as plagiarism". I think they are now checking the details and will inform me any time soon. – offeltoffel Jul 06 '20 at 09:48
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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.

Anonymous Physicist
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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 02 '20 at 09:02
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    @Wrzlprmft A simpler explanation would be that the academic editors do not exist. – Anonymous Physicist Jul 02 '20 at 09:07
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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 02 '20 at 09:14
  • 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 02 '20 at 09:15
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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 02 '20 at 09:35
  • @AnonymousPhysicist: Why? Unless there is evidence to believe that the journal ought to be "most esteemed", there is no reason to hope that it is so or remains so. – user21820 Jul 04 '20 at 09:11
  • @user21820 The evidence is offeltoffel said so. – Anonymous Physicist Jul 04 '20 at 09:28
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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.

NCFrank
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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 04 '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 06 '20 at 09:37
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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 06 '20 at 14:08