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So, I want to structure the most important parts of the site. I have main page, where there is a grid/wall of thumbnails. On the side, there is latest comments.
Is it a good idea to structure them as UserComments? Or will the engines think that those are the comments for that page?
You should use Comment instead of UserComments.
UserComments is for the action/event of commenting, while Comment represents the published comment itself. (You’ll often find that UserComments is used although it’s not appropriate; that is because Comment was introduced later.)
Neither Schema.org nor Microdata define which conclusions can be drawn when a page contains these annotations, i.e., it is not defined that only the main content should be annotated.
If a consumer (like a search engine) draws a conclusion like "If I find Comment markup, I assume that these comments are about the main content of the page", it’s quite adventurous: it would probably be wrong with this conclusion more often than not.
Instead, such a consumer should look for a property relating this Comment to something. For example, when it finds
it can conclude that these are comments about the webpage.
When there is no property, the only thing that can be concluded is: There is a comment.
So, it’s perfectly fine (and it can also be useful) to mark up any content that is shown on the page, not only the main content.
<aside>, then using schema usingitemprop="commentTextanditemprop="commentUser".