Jon Udell wrote a blog February 9th, 2018 he named Preserving comments from PubMed central about PubMed announced discontinuation of PubMed comments because it wasn´t used enough (only 6.000 articles of the 28 millions had gotten comments).
In the blog https://web.hypothes.is/blog/archiving-pmc-comments/ Jon Udell tell how they did build a tool to extract comments from an article and then being able to sync it across different copies of it at journal websites, PubMed and PubMedCentral. I hope this development will go on and will also get to the repositories.
You can browse here the comments they did extract from PubMed, they are all filtered by PubMedCommonsArchive tag which they added to every annotation when they did import it. They also tagged each comment with unique PMID of related document. And now everyone can browse and search all comments by using a PMID tag.
At the end of the blog Jon Udell say :
“In our strong opinion, all article feedback, commenting, review or other collaboration systems should as quickly as possible adopt W3C standards for web annotation, so that we can begin to move towards an integrated and open framework for engagement across scientific and scholarly literature.”