Annotating Manuscripts with

A few months ago, AGU introduced a new feature in GEMS – annotating the merged PDF of the manuscript. Senior AGU Pubs staff wrote an Eos Editors’ Vox article about it. AGU has partnered with, an online annotation tool, so that reviewers can highlight text and insert comments. Editors can then add additional comments before making a decision about the paper. The comments are labeled “reviewer 1,” “Editor,” etc., so that the author can identify which of the assessors made the remark. During the revision process, authors can respond to these comments directly in the annotated PDF.


            I have used it a couple of times and I have seen ~10 reviewers use it over the last few months. I think it works really well, so it is it time to publicize this feature and make the community aware of this powerful resource.

When you agree to review a manuscript, you will see this new section on the review page:


It’s just below the link to retrieve the paper and the link for submitting your review. When you click on it, you get a new browser window with the manuscript PDF:


This page already has several sections of text highlighted with example comments written. There are controls across the top bar for navigating around the document. When you highlight some text, a small pop-up window appears below it with the word “annotate” in it:


This opens a text box in the right-hand column in which you can type your comment:


The “You” at the top indicates the originator of the comment, then the highlighted text is repeated, and then a box for writing your comment, including rich text features like inserting hyperlinks, images, and LaTeX-based equations. Along the bottom of the text box is a row of buttons for specifying the type of remark you are making. Is it an overview comment? Pick “Summary.” Do you want to designate it as a “major” or “minor” concern? Go for it. Are you suggesting a small English usage correction? Then pick “Edit.” Are you suggesting a new reference or two, or commenting on a figure? Click that button, then. Finally, there is a “Confidential?” button that you can click if the remark is just to the Editor and not meant for the author. I promise to look through the comments and read these.

Back on the main reviewer page, you can actually see if there are annotations on the “annotated merged PDF.” It should appear as a new link, “Show Summary Table,” like this:


When you click on this, all of the comments in the PDF are shown:


Nice, huh?

Note that you still need to click the link on the main reviewer page to complete the review:


You should answer the pull-down-menu questions and fill in any comments you want in the review text box. It is helpful if you, at the least include a sentence like, “Please see my detailed comments in the online annotated PDF.” This reminds the Editor to go to the annotated PDF and see your comments there. It is also helpful to include a short paragraph summary of your review there. In fact, you can make your review a hybrid of the two, with major comments in the review text box and specific comments embedded in the annotated PDF.

In addition to the Eos article and this blog, there are also more detailed author instructions, reviewer instructions, and even editor instructions at the AGU website. The website also has a really good tutorial. Also, one caveat: it is an interactive web-based tool, so you have to be online to use it.

Also, this whole thing is optional. You don’t have to use it. So far, I’d say that most reviewers do not use it. But most reviewers could be using it, so please consider it. Many reviews include line-identified comments, and this new feature should be easier than typing the location coordinates into your review.


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