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The comments and tracked changes can be made visible in the PDF output by setting the show.changes.and.comments transformation parameter to yes.

Figure 1: Chemistry Annotations in Acrobat Reader
By default, they are shown as PDF text annotations (sticky notes). These are graphical markers in the document content and are also listed in the Comments section when opening the output file in Acrobat Reader.
Note: Comments with the Mark as Done flag selected appear with a checkmark in the Comments section and with a Completed label ().

To avoid rendering the elements as PDF annotations and show them as footnotes instead, you can use the show.changes.and.comments.as.pdf.sticky.notes transformation parameter set to no.

The comments and changes are included in the merged map file either as XML elements (<oxy-insert>, <oxy-delete>, <oxy-comment>, <oxy-attributes>) in the case of the XML merged map, or as HTML elements with similar classes (oxy-insert, oxy-delete, oxy-comment, oxy-attributes) in the case of the HTML merged map. Sub-elements contain meta-information about each change.

Tip: These elements are automatically recognized and transformed in PDF annotations when using Chemistry as PDF processor.
Note: The inserted text, deleted text, and deleted markup are included in the sticky notes.