Tuesday 12 November 2013

PubMed commons: how will we use it?

PubMed commons is hoping to create somewhere for researchers to "share their opinions about scientific publications", it is going to be for "open and constructive criticism and discussion of scientific issues" and will "depend on the scientific quality of the interchange". Your comments are made available under a CC license so everyone can reuse them and comments are moderated (I already saw one that had been removed).

Users need to register with their real identities and are encouraged to leave short posts with references if necessary (see how to get your comment noticed below). Don't quote unpublished results or be offencive (racist, sexist, overtly commercial, etc).

There are currently 318 papers with comments (has_user_comments[sb] search term on PubMed).  Only 10% of these have more than 2 comments, 5 have 3 comments and 3 have four or more comments. Early days!

Many of the comments are detailed academic evaluations of the work. Some are personal opinions and some are the lead authors summary of findings. Hopefully these comments will continue to come from the same direction; as other academics review work against alternate views, as authors update their own comments to reflect additional work and hopefully as more people say they like or otherwise the work described.

I'm not sure when the pilot phase closes and PubMed commons opens up to everyone. I can only say the sooner the better and well done to PubMed for what I believe is going to be a useful addition to literature searching.

How to join PubMed commons: Joining instructions can be found at the PubMed website, it feels a bit like the early days of gMail when only a gMail user could invite new people onto the system. I think it could grow very quickly under this model but the pilot should conclude and then access will be universal. After all not everyone is funded by NIH or Wellcome!

How to get your comment noticed: One detail I am unclear on is why the PMID is being used rather than the DOI (which I like and have posted about previously). PubMed recommend you simple use The use of the latter means any comments can be picked up using a single identifier for a piece of work. Systems like Altmetric are making metrics available that are enlightening for researchers to see. How much is a paper making the news, blogosphere and now perhaps what academic commentary is being added. I want to go to one place for this information and hope Altmetric (or someone else) can become that single destination.

What's on PubMed comons? Of the papers receiving most comments (early days don't forget) a couple stood out to me:

The 2011 Science paper that has already attracted a lot of negative attention, and had a response posted by the authors on Science, A bacterium that can grow by using arsenic instead of phosphorus.

A PNAS 2005 paper; Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, a very high-impact paper on anyone who's been running microarrays, RNA-seq and similar for most of the last decade.

Will PubMed commons be just another place to leave comments and will a site like Altmetric become the place we go to gather data on papers as they "scrape" information from multiple sources? I guess time will tell, for now we'll just have to keep looking and listening for comments on our research papers. You can follow PubMed on Twitter @PubMedCommons.


  1. Thanks James. I just added "has_user_comments[sb] Forshew T" to my list of saved searches. It seems like something we should potentially all do so we can see if people comment on our papers.


  2. That's a great idea Tim; I've done the same! Now if only Altmetric allowed you to get something similar through your ORCID ID?

  3. KODAMA: a new data mining method


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