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Often, one gets a notification email with, typically 2 to 5, review reports compiled together and one would respond to each of these reviews with a list of "quote/response" items (if needed, referring to the revised manuscript) in form of a response letter. Now, facing the case of both an email with review reports and a commented PDF basically replacing/extending one of the reports, how would I pragmatically write the response letter? Should I respond to the PDF-based review ...

  1. by copying each of the PDF comments into the main response letter, add a reference to the commented PDF, and add my response item?
  2. with another commented PDF (i.e. my comments would be next to the reviewer's comments and, if needed, refer to the revised manuscript) and refer to this PDF in the corresponding section of the main response letter?

The first solution sounds more coherent to me while the second solution may be more easily usable by editors or reviewers. Apart from that more general guidance, I haven't found anything. This might be a bit of a trivial question but I appreciate any suggestions about best practices.

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As one of the people who writes reviews in the form of annotated PDF files + a summary review, I think I'm in a good position to answer this question :-)

At least in my case, annotations in the PDF are often of relatively small points. I expect you to address all points raised in annotations, but you don't have to prove it to me by mentioning them individually in your response. Many will be typos/grammar annotations, some about missing axis labels, etc. In your written response, just mention somewhere that all of the points raised in annotations in the PDF that are not specifically addressed in your response have been taken care of -- that's enough for me, and likely the editor.

That leaves maybe ten longer comments in the margins of the PDF. If you think that they are worth addressing individually, copy the text into your response and add your reply. That should be easy enough to do.

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    Just curious: how do you ensure that your annotated PDF review is anonymous? In my experience, PDF-producing software tries to put your name everywhere, which is a pain when you need to stay anonymous. – Federico Poloni Jan 8 '20 at 10:35
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    Most of the time I just don't care if someone finds out about my name if they must because I'm confident in my review. But I have checked whether my tablet puts my name into the PDF and it doesn't seem to. – Wolfgang Bangerth Jan 8 '20 at 16:41
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Either approach is fine.

The quality and clarity of the responses is more important than the format.

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I wouldn't jeopardise the response. I would neatly adress all the points raised by the referee as usual in a single letter addressed to the editor, clearly indicating when you respond to criticisms or suggestions only stated in the pdf report by quoting or grouping them (depending on their importance, as usual).

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