About PubMed Commons Team

PubMed Commons enables authors to share opinions and information about scientific publications in PubMed, the U.S. National Library of Medicine's database of the biomedical literature.

PubMed comments & their continuing conversations

bubbles_3aWe have many options for communication. We can choose platforms that fit our style, approach, and time constraints. From pop culture to current events, information and opinions are shared and discussed across multiple channels. And scientific publications are no exception.

PubMed Commons was established to enable commenting in PubMed, the largest biomedical literature database. In the past year, commenters posted to more than 1,400 publications. Of those publications, 80% have a single comment today, and 12% have comments from multiple members. The conversation carries forward in other venues.

Sometimes comments pull in discussion from other locations or spark exchanges elsewhere.Here are a few examples where social media prompted PubMed Commons posts or continued the commentary on publications.

Debating disease association

On June 3, 2016, Daniel MacArthur took to Twitter to express his skepticism of a report describing an association between a gene mutation and familial multiple sclerosis published in the journal Neuron. His critique stirred a bit of interest. A few days later, he posted a comment, co-written with Eric Minikel, to PubMed Commons. MacArthur and Minikel highlighted, “Enrichment in cases over controls is one important criterion for establishing pathogenicity of sequence variants.” The comment prompted more discussion on Twitter.

Over the following days, author Carles Vilariño-Güell responded, and MacArthur and Minikel replied. Shortly Chris Cotsapas posted a comment on behalf of the International Multiple Sclerosis Genetics Consortium. His comment summarized an attempt to validate the findings, linking to results posted in a bioRχiv preprint. With Simon Heath, Daniel Weeks noted further concerns in an August comment on the journal’s website, which he linked from PubMed Commons.

As the critiques unfolded, some readers commented on blog posts highlighting the results, (such as here and here) to point to the comments on PubMed. In September, STAT published a story reviewing the concerns that had been raised on PubMed Commons and elsewhere. In October, Neuron published letters from the International Multiple Sclerosis Genetics Consortium and Minikel and MacArthur, as well as a response from the authors. In an accompanying editorial note, the editors remark that the peer-reviewed letters offer “an important complement to other forms of commentary” including social media, PubMed Commons, and the journal’s online comments section.

Comments also sparked discussion of topics beyond the specific gene variant in question.

Self-correcting statements

In July 2016, a publication co-authored by Thomas Nichols reported on an artifact that might give rise to high false-positive rates in functional magnetic resonance imaging (fMRI) analyses. Across blogs and professional publications, there was consideration of what the findings meant for neuroscience research. But some in the community thought results were being too broadly extrapolated to all fMRI studies, not just the specific issues examined.

As the publication was discussed online, the authors recognized that some wording was being interpreted in ways they had not anticipated. So they asked to publish an erratum. That was initially rejected by the journal, since there was no change to the results or conclusions. Nichols published the note on his blog. Following an exchange on Twitter, he subsequently posted a comment on PubMed Commons to make a more circumspect significance statement.

At least one blogger updated a post to reflect the authors’ statement.

Although the journal ultimately published a correction a month later, PubMed Commons enabled authors to rapidly communicate a reframed interpretation of their work.

Replicating and reviewing search strategies

Comments can initiate discussion of specific results and interpretations. But they can also serve as a jumping off point to evaluate approaches and highlight practices.

Literature search strategies lie at the core of systematic reviews and meta-analyses. Melissa Rethlefsen posted a comment describing an attempt to replicate the search strategy reported in a meta-analysis. She noted key missing information such as date ranges. She concluded: “This study highlights the need for more accurate and comprehensive reporting needed for search strategies in systematic reviews and other literature search-based research syntheses, and the need for better peer review of search strategies by information specialists/medical librarians.”

One library used this example to encourage the use of structured reporting guidelines for systematic reviews and meta-analyses.

Another library used the comment to illustrate the importance of reviewing search strategies. And medical librarians and researchers chimed in on Twitter.

Extending the reach of scientific discourse

As you browse the web, you might just run across a mention of a comment on PubMed. Blog authors and readers might mention comments, as they have about a genetic variant associated with body mass index , ‘bad luck’ and cancer, or the occurrence of amphetamines in water systems. They might even appear in the references list, such as a roundup of publications on cancer risk or a look at psychological debriefing after traumatic events. Perhaps the most talked-about comments were those from Jennifer Doudna and Emmanuelle Charpentier on a perspective of the history of CRISPR. The comments were shared and discussed on social media. They were also mentioned in several blog posts and articles, including ones from news outlets such as the Washington Post.

PubMed Commons offers a key place to quickly anchor critical points for future readers to see­­—in one of biomedical science’s most heavily used resources. On a typical day in 2016, 1.6 million users ran 2.5 million web searches on PubMed and viewed more 8 million records.

Through October 31, 2016, PubMed Commons had 10,632 members. They’ve posted 5,739 comments to 4,595 publications. Want to join in? Check out our Get Started page for more information!

The PubMed Commons Team

Commenting on PubMed: A Successful Pilot

endpilot_blogimgWe are pleased to announce that PubMed Commons is here to stay! After developing and piloting the core commenting system for PubMed, a pilot of journal clubs was added. And we have completed a major internal evaluation of the use of the Commons. We aim to publish that soon, so stay tuned to this blog or Twitter for news on that.

PubMed Commons provides a forum for scientific discourse that is integrated with PubMed, a major database of citations to the biomedical literature. Any author of a publication in PubMed is eligible to join and post comments to any citation.

More than 9,500 authors have joined PubMed Commons – and they have posted over 4,000 comments to more than 3,300 publications, mostly on recent publications. Commenting has plateaued, so the volume is low. But the value of comments has remained high. And comments often attract a lot of attention.

About half the comments are on clinical or health-related publications. Members have been using PubMed Commons to:

  • Update and expand the public record, for instance by pointing to new data, relevant publications, or alternative interpretations
  • Note corrections and retractions to publications
  • Post discussion and critique, either directly or via links to blog posts and other platforms
  • Provide links to datasets, code, or publicly accessible versions of publications
  • Call attention to issues affecting reproducibility, such as cell line misidentification

Authors posting to their own publications contribute about one in five comments. About one-third of these have been replies to questions or discussion from others. Since the PubMed Commons Team began notifying authors of comments on their publications, the proportion of comments with author replies has increased. However, the rate of reply remains below 10%. We will keep working on ways to encourage more author response.

Just a year ago, we introduced a new mechanism to capture the synthesis of journal club discussions of scientific publications. PubMed Commons Journal Clubs have full commenting privileges and profile pages to provide background information about the club. To date, 20 journal clubs have joined. These institutional, virtual, and hybrid journal clubs represent a range of clinical and biomedical disciplines. They have become a critical and vibrant part of PubMed, and we are planning more support for this initiative.

PubMed will shortly turn 20. It has become a major resource for finding biomedical and health-related literature. There are now more than 25 million citations. And there were more than 2.7 billion searches in the last year – that’s more than 7 million searches a day.

That means that comments have a large potential audience, and the interest in them is growing. Visits to the PubMed Commons homepage have nearly doubled, from 1.2 million in the first half of 2014 to 2.3 million in the first half of 2015.

We believe the commenting function addresses a critical need, for PubMed and for the development of biomedical research. So a big “thank you” from us to everyone who has contributed their time and energy to supporting the Commons and commenting at PubMed.

Just because the pilot has ended, doesn’t mean PubMed Commons will stop evolving. With the pilot over, we’re working on an application program interface (API) that will enable hosting of PubMed comments on third-party sites. And other new features are in the pipeline. Meanwhile, anyone can submit suggestions and feedback by using the “Write to the Help Desk” link at the bottom of NCBI pages.

 

Ready to get involved? Visit our Getting Started page to learn more about how to join and participate in PubMed Commons – or start here if you would like your Journal Club to join in.

 

The PubMed Commons Team

Signposts from research to resources

Woman working at computerFrom repositories to blogs, the web has expanded means to share information and resources widely. Access to data and code enables other researchers to check published analyses and undertake new ones. Having another way to look at results can help people connect with them and deepen understanding. PubMed Commons members are tying these pieces back to publications by adding external links to PubMed records.

Tagging inputs 

High-throughput assays generate heaps of data, which can require custom software tools to process and analyze. Some authors are annotating current locations and updates for data and code via PubMed Commons.

Proteomics studies approach a wide range of questions about proteins and pathways, often with mass spectrometry data at the core. Author David Simpson provides the identifier and URL to access the dataset for a recent publication. Attila Csordas has also connected several proteomics articles to deposited data.

Patrick Schloss and colleagues published an approach for characterizing microbiomes using a particular high-throughput sequencing platform. He links to “a fully executable version” of his paper. The repository includes the R code, as well as raw and processed data, so that users can reproduce results in the publication.

With the end of Google Code on the horizon, researchers are moving projects to new locations. Pedro Mendes has migrated code for a tool used in modeling of biochemical networks to GitHub. He’s added a comment to point to the code’s new home.

Sometimes authors will update code and append new options. Ross Lazarus summarizes features added to a toolkit for high-throughput biology workflow software. He also includes a link to the new version.

Adding dimensions

Three-dimensional structures of biological molecules can offer useful insight into how proteins function. But as figures in papers, structures can fall flat. Some are using PubMed Commons to restore depth.

Michael Cianfrocco and colleagues solved the structure of a transcription factor complex bound to DNA. He provides a link to FigShare where users can download files for a visualization program. They can then dive into the structure and even create their own figures.

Sandra Porter links to a blog post, where she writes, “One of the most amazing things, to me at least, is how spider silk changes from a liquid form, inside the spider, to a solid, strong material that we see in their webs and other constructions.” She shows readers how to use their tablets to explore the structure and properties of a protein in spider silk that permit this change.

Mary Mangan offers a resource for a literal hands-on approach. She used data from an X-ray crystal structure to create a 3D-printable model of γ-hemolysin, a pore forming protein from Staphylococcus aureus. She points readers to the model on the NIH 3D Print Exchange.

Have something you want to add to a publication? Any author of a PubMed-indexed publication is eligible to join PubMed Commons. Learn how! And check out more examples of how PubMed Commons is being put to use.

The PubMed Commons Team

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. 

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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 pubmed.commons@ncbi.nlm.nih.gov.

The PubMed Commons Team