Introducing PubMed Commons Journal Clubs

Around the world, the journal club is a cornerstone engagement with the scholarly literature. Whether in face-to-face meetings or on social media platforms, researchers, physicians, and trainees gather to debate and converse about publications. Participants share their views on methods and interpretations of results. They discuss how publications fit into a broader context or might inform their own research or practice.

In short, the journal club can represent a major intellectual investment – and a long-standing form of post-publication evaluation.

Yet often, the analyses and ideas don’t travel far beyond core participants. Digital records and virtual journal clubs can help deliver the discourse to others. Still, wouldn’t it be fantastic if more of us could see what these groups have to say?

Today we’re excited to announce the launch of PubMed Commons Journal Clubs. These accounts will allow groups to establish their own identity on PubMed Commons. Journal clubs will be able to share key points, questions, and summaries from their discussions – right below citations in PubMed.

Bringing local discussion to the global Commons

Gary Ward is a professor in the Department of Microbiology and Molecular Genetics at the University of Vermont. (He is also a member of the external working group providing feedback on PubMed Commons.) His lab studies Toxoplasma gondii, a protozoan parasite. It’s widespread among humans and other mammals and can cause serious illness for those who are pregnant or have weakened immune systems.

UVM Toxo Journal Club covers work on parasites like Toxoplasma gondi (Image courtesy of Aoife Heaslip)

UVM Toxo Journal Club covers work on parasites like Toxoplasma gondii.

Ward also facilitates the University of Vermont (UVM) Toxoplasma Journal Club, a group of grad students, postdocs, technicians and faculty who do research on T. gondii. “We try to review both classic papers (why is this a classic in our field?) and very recent findings in the world of parasite cell biology.”

“We each take turns picking a paper and leading the discussion,” he explains. Last year, the group added a new step. “Immediately after the journal club, the discussion leader is responsible for drafting a PubMed Commons comment that summarizes the key points of the discussion. The comment is revised based on feedback from the group and then posted.”

Ward notes the direct benefit of this process for participants. “Having to summarize our meeting in the form of a comment forces us to distill the many things that were discussed into the two or three most important points. The ability to focus one’s critique/comments in this way is a great skill for grad students and postdocs to learn, and for the rest of us to practice.”

He also thinks that journal clubs have something more to offer to the scientific community at large. “Other than the journal club setting, how often does a paper get read critically from beginning to end by 10-12 informed readers who then discuss it at length as a group?  This kind of collective discussion is a great way to surface the strengths and weaknesses of a study and to identify connections to other work.”

“Posting journal club comments in PubMed Commons adds depth to the literature and may give the reader a different perspective on the work,” Ward explains. “They will be particularly useful when they stimulate the authors to engage in a PubMed Commons dialog. If our journal club had a particular question about the paper, it is likely that other readers will as well.”

The UVM Toxoplasma Journal Club has a great example of just how that can happen. 


Expediting lab-to-lab communications

Three thousand miles away from Burlington, Vermont, Markus Meissner’s group at the University of Glasgow had worked out a method to target genes in T. gondii for conditional deletion. They applied the approach to look at how the parasite infected host cells. Meissner’s group found that actin was essential to T. gondii survival – but not because the parasites couldn’t invade host cells. Rather, they argued, the parasites die because they lose a specialized part of the cell called the apicoplast.

“In our discussion of this paper,” Ward notes, “a new graduate student in the group suggested a great idea on how to test this hypothesis.”

The apicoplast is essential for survival of Plasmodium falciparum, the parasite that causes malaria. However, blood-stage P. falciparum can live without an apicoplast if supplied with isopentenyl pyrophosphate (IPP), which is normally produced in the apicoplast.

The journal club asked in their comment: Could T. gondii lacking actin survive if given IPP?

Meissner replied. His lab had considered the experiment but scrapped the idea after learning from other experts that IPP treatment doesn’t have the same effect in T. gondii as it does P. falciparum.

This instance illustrates how PubMed Commons can initiate useful exchanges. “Now anyone wondering if IPP rescues an apicoplast defect in T. gondii can discover that it doesn’t,” says Ward. “That information had not previously been captured, but now it is in the form of a PubMed Commons comment.”

Calling journal clubs to join the discourse

NephJC brings discussions from the nephrology (& related specialties) Twitter community.

NephJC brings discussions from the nephrology (& related specialties) Twitter community.

With PubMed Commons Journal Clubs, we’re hoping to see groups and individuals engaging on PubMed Commons and beyond. We’re pleased to welcome the UVM Toxo Journal Club, NephJC, and CREBP Journal Club as our first PubMed Commons Journal Clubs.

To encourage connections, PubMed Commons Journal Clubs will have profile pages on PubMed Commons. These pages will provide descriptions of the groups and ways to connect with them outside PubMed Commons (click the Journal Club images in this post to see their pages). We’re also starting a Facebook page to offer a space for group members to start sharing their ideas (link coming soon). We’ll be exploring other ways to help groups network, as we build and develop the PubMed Commons Journal Clubs community.

CREBP Journal Club hails from the Centre for Research in Evidence-Based Practice at Bond University.

CREBP Journal Club at Bond University looks at the gaps between evidence and current clinical practice.

PubMed Commons Journal Club accounts are currently open to journal clubs discussing literature for research, graduate and postgraduate education, or continuing professional education. Applications will need to be supported by PubMed Commons members who participate in the group’s discussions. For more information or to apply for a Journal Club account, email

The PubMed Commons Team

Unveiling a new look – and more – for PubMed Commons

PubMed Commons set the stage for commenting on any publication in PubMed, the world’s largest searchable database of biomedical literature. Lately we’ve been tackling infrastructure and design to improve the user experience and support the PubMed Commons community. Those developments are now live on PubMed and PubMed Commons. Here’s what you can expect from the PubMed Commons update.

Center stage

Some changes are likely to jump out for frequent PubMed Commons users.

@PubMedCommonsWe’ve adopted new artwork for our blog, Twitter account, and homepage. We’re going for a clear, unified identity across platforms, one that we hope will be recognizable wherever you see us.

We’ve made some modifications to streamline our homepage. We’ve consolidated information about joining and using PubMed Commons in a single page to help you get started. You’ll also find a synopsis of our most recent blog post at the top of our homepage to help you stay up-to-date on PubMed Commons.

For several months, comment rating has given members the chance to weigh in on what comments they find useful. Visitors to PubMed can see these ratings alongside comments. Ratings are a key element in calculating the comment and commenter scores that determine the appearance of comments in the “Selected comments” stream on our homepage.

Some new site modifications will highlight your contributions to PubMed Commons. On our homepage, “Top comments now will feature the top three recent comments. On PubMed records, “Selected comments” (from our homepage stream) prompt the appearance of an icon above abstracts, directing readers to comments below.

This new icon will appear above some abstracts in PubMed.

This new icon will appear above some abstracts in PubMed.

For a while, we’ve selected highly-rated comments to post to our Twitter stream. Starting today, the most recent tweet about a PubMed Commons comment appears on the homepage for PubMed searches. Check it out!

Behind the scenes

Some key changes in the PubMed Commons development won’t be visible on the PubMed Commons site. We’ve improved our “Invite an author” function. It looks the same as before, but we hope you’ll encounter fewer errors when inviting authors to join or comment. (If you do encounter errors, please let us know by using the “Write to the Help Desk” link, found at the bottom of every NCBI page.)

inviteIn response to community feedback, we are also notifying corresponding authors of comments on their publications and inviting them to join PubMed Commons. We’ve been at it for two months, and we’re encouraged by the increase in author responses. We will continue our notification process, but we still encourage members to notify a publication’s author(s) when commenting.

More to come

We’re not done yet. In May, an external working group for PubMed Commons was established. The members offered great feedback and ideas on where PubMed Commons is and where it’s going. But more on that later…

The cornerstone for the continued growth of PubMed Commons is you! Here’s how you can get involved:

  • Learn more about the PubMed Commons pilot.
  • Are you an author of a PubMed-indexed publication? Join PubMed Commons!
  • Already a PubMed Commons member?
    • Post a comment! Log in to My NCBI, find a PubMed citation, and start typing. Not sure what to post? Check out these examples of how authors have been using PubMed Commons.
    • Rate comments. It only takes a moment, and as we discussed above, you can influence what’s highlighted on PubMed Commons – and PubMed.
    • Invite your colleagues!
  • Finally, help us spread the word about PubMed Commons!

Thanks for your support and contributions to PubMed Commons. We look forward to seeing where this community takes us next.

The PubMed Commons Team