Journal rejected my paper because contents of paper are in PhD thesis I have submitted a journal paper to a journal four days ago and today I received an email informing me that it has been rejected. The only reason for this is: &quot;About 70 % of the article is similar to other documents&quot;.
I know my paper and I know that I haven't copied it from anywhere else. There is a conference version of the paper, but it is different, plus it is 6 pages long, while the journal is 15 pages long, so since 6/15 = 40%, it doesn't add up to 70%, and this is not the reason for rejection.
The real reason is that my PhD thesis is available online (it is mandatory at my university to add it to an open repository if I want to graduate). I graduated 3 months ago, and in fact the last chapter of my thesis consists in the paper that was rejected now. However, I was always told both by my supervisor who is a full professor with 25 years of experience (and Associate Editor of top-notch journals) and by many other people that it is not a problem to submit a paper based on an already published PhD thesis, as journals should not consider the thesis as a paper. Therefore, I am very surprised by the decision made by the editor. What should one do? Wait to graduate until the paper is accepted? That is simply ridiculous.
Has this occurred to any of you? Do you know how journals behave in this case? I once reviewed a journal paper which was literally copy-pasted from a chapter of a PhD thesis of a student. I contacted the editor who had sent me that paper asking what to do and he mentioned that it is a standard and common practice and it shouldn't be considered self plagiarism. So, once again, I am very surprised by the decision made.
EDIT: as asked in the comments, here is the email I sent to the editor:
Dear Professor XYZ,
I am contacting you regarding the submission of my paper to the journal ABC123. As in the subject, the reference number of the manuscript is XXXYYYZZZ. Today I have received an email notifying me that my paper (submitted only 4 days ago) has been rejected. You may find the email attached to this email. The reason for this is: “About 70 % of the article is similar to other documents”.
The possible reason for this very high similarity is threefold:

I have published a related conference paper before, containing preliminary results and much less content in general. However, that conference paper is 6 pages long, while the paper submitted to ABC123 is 15 pages long. Therefore, it is mathematically impossible for the conference paper to be the reason of the &gt; 70% similarity, since 6/15 = 40%;
The paper has been uploaded on arXiv. This was done the same day in which I sent the paper to your journal. However, this is allowed by Elsevier, as explained here;
The contents of the paper are part of my PhD thesis, in particular, of Chapter 5. This is what probably results in the highest similarity, as the article submitted to your journal is based on this chapter. However, Elsevier’s policy with respect to PhD thesis is the following: “Elsevier does not count publication of an academic thesis as prior publication”.

I have run a plagiarism check myself, you can find it attached to this email. This confirms what I have said so far: the similarity of my article is related to my PhD thesis, not to any other previously published works.
Given the above explanations, I would kindly ask you if you could reconsider your decision. The plagiarism check returned indeed a similarity higher than 70%, but, as explained above, this is most likely related to my PhD thesis. However, Elsevier does not count PhD thesis as prior publication. Therefore, my paper submitted to ABC123 respects Elsevier’s policies and should therefore be considered a new publication.
Thank you for your consideration.
Best regards,
cholo14
Email the editor, explain that their automated plagiarism detection system has seemingly gone awry, inadvertently flagging your PhD thesis.