PubMed had an own comments feature “PubMed Commons” which had been shut down in 2018.
NIH announced it will be discontinuing the service — which allowed only signed comments from authors with papers indexed in PubMed, among other restrictions — after more than four years, due to a lack of interest.
But there is no lack of interest, if we look at the ever increasing rates at PubPeer – the counter today is 122.000.
The main difference between PubMed Commons and PubPeer is the chance of submitting anonymous comments. While I also see a risk of unjustified accusations or online stalking, I believe that the current PubPeer coordinators handle this issue very well. We can post only issues that are obvious, directly visible or backed up by another source.
We should be aware also that 80% or even 90% of pre-publication peer review is also anonymous. Anonymity guarantees protection for the reviewer from retaliation and discrimination. So why shouldn’t 80% of post-publication peer review als be anonymous? There was an interesting Scientific America article back in 2020 “Anonymous Peer Review: Truth or Trolling?”
But all of us have experienced, perhaps more often than not, the distorting effects of anonymity when it results in prejudiced reviews. In some cases, these can have devastating effects on early careers and hit hard at fragile self-esteem. As with trolling in social media, anonymity in peer review is sometimes used to say those things that would never be said if reviewers had to reveal their identity.
That may be true if an anonymous reviewer prevents a paper from being published. But the situation is completely different with post publication review as everybody can check the sources.
IMHO the best approach is the upload of every manuscript to a preprint server. Journals are scouting the most interesting papers, pay 5-6 reviewers for reading it and discuss it afterwards
One particularly interesting approach is at the journal eLife. There, responses are not the usual handful of sometimes contradictory opinions. Instead, reviewers are allowed to communicate with each other in a chat room, and they all come to a single, unified opinion (yes, like a jury).
Back to PubPeer. The exceptional increase in the last few years clearly indicates the importance of the service. Whenever PubPeer has reached 1 million entries I hope it will be merged into Pubmed.
And please note – in former times post publication review was the norm if we read about Einstein and the Physical Reviews
For instance, the Annalen der Physik, in which Einstein published his four famous papers in 1905, did not subject those papers to the same review process. The journal had a remarkably high acceptance rate (of about 90-95%). …
[Einstein] and his younger colleague, Nathan Rosen, sent a paper on gravitational waves to Physical Review … John Tate, the editor of the journal, hesitated over Einstein’s paper for a month. He then send it to a reviewer for comments … Here is how Einstein reacted:
We (Mr. Rosen and I) had sent you our manuscript for publication and had not authorised you to show it to specialists before it is printed. I see no reason to address the – in any case erroneous – comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere.