What’s the Answer? (commenting at PubMedCommons)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted Biostar post is about commenting. There’s a new feature at PubMed that allows (some) people to comment on the entries. The question is: will it be valuable, or descend into a swamp of YouTube-esque absurdity….?

News: PubMed Commons : a system that enables researchers to share their opinions about scientific publications

via Pedro Beltrao: https://twitter.com/pedrobeltrao/status/392668221993529345


PubMed Commons is a system that enables researchers to share their opinions about scientific publications. Researchers can comment on any publication indexed by PubMed, and read the comments of others. PubMed Commons is a forum for open and constructive criticism and discussion of scientific issues. It will thrive with high quality interchange from the scientific community. PubMed Commons is currently in a closed pilot testing phase, which means that only invited participants can add and view comments in PubMed.

NCBI Commons features

Pierre Lindenbaum

So as I noted at Biostar, I decided to kick the tires (as I am wont to do every time I see new software). I left a comment on the Biostar paper entry, and I also tried the “invite author to comment” feature. Seemed to me that feature could either be handy to contact people, or an invitation to spam. But it turns out you need to know the author’s email anyway, so it’s not really much more useful than your own inbox.

I realize that you can’t see the comments unless you are registered for this and logged in to MyNCBI apparently. I went back with another browser not logged in and you can’t even tell there’s a comment. But I’m told this is just the pilot phase and that comments will be broadly visible later. Here’s what I left in case you don’t have a login:


Who had time to vote this down already–I just put it on there less than half an hour ago?? Yeah, that’s friendly and makes me want to participate.

If you are logged in to NCBI, you can identify papers with comments by the little icon beneath:


So far the early adopters are largely people I recognize as chatty and connected folks already :). And they are often linking to their own blog posts about whatever their issue was. On this database citation paper Martin Fenner linked to his related plugin. Pierre Lindenbaum added the new source for the software from a paper he published way back–that’s a great use of the comments.

With that, I’m interested to see if this becomes useful. In the comments at Biostar you should click the link to the discussion at Retraction Watch about this. Very interesting perspective and comments below that. I don’t know if I agree with them all, but the discussion is interesting on both sides.

If you want to join, there’s now a step-by-step guide for this: http://ncbiinsights.ncbi.nlm.nih.gov/2013/10/23/joining-pubmed-commons-a-step-by-step-guide/ (h/t Francis Ouellette).

If you have a paper in PubMed, and you want an invitation, I’m willing to try to get you one. Give me your PubMed paper ID in the comment body, and the email address you use for your NCBI account (you can put that in your comment as the “email” line that I can see in the backend of the post but isn’t public). I’ll try it out. This seemed to work last night for someone that I invited. But as it’s beta I can’t promise that will work–I only have N=1 so far.