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. 


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

Refining & revising research on the public record

179024690The life of a research project often doesn’t end when a publication appears in a journal. Experiments continue. Errors are found. Supporting or refuting data is published. Alternative explanations emerge… So PubMed Commons members are posting updated and complementary information to keep work current.

Honing interpretations

Consider, for example, Daniel Haft’s reflection on his publication from 2009. He identified some peptides in two Bacillus strains that he referred to as putative “bacteriocins”. The term describes bacterial peptides that are toxic to related strains. Use of the term was “overconfident”, he notes, “…given the lack of evidence then that these heterocycle-containing natural products were toxins rather than, say, peptide pheromones.” But now results from another group suggest he was on the right track after all.

Andrew Sharp’s group studies how genome structure relates to human disease including X-chromosome inactivation. He considers how a new publication describing DNA methylation in development might be relevant to their own work.

Meta-analysis can show patterns and discrepancies between results from different studies. The data can be calculated in different ways. Valeria Fadda provides alternative data visualizations by posting forest plots for risk differences from published meta-analyses.

Dopamine is a central player in addiction in rodents. Many factors, including where it acts, influence the effects of this neurotransmitter. Roy Wise notes how his group’s work supports recent findings on the consequences of location and what this might mean for the field.

“The mechanisms for establishing, maintaining, and reinstatement of cocaine self-administration have been studied extensively, but have not yet led to a proven medication for cocaine addiction,” Wise remarks. “Perhaps it is time to turn attention to the endogenous mechanisms for what appears to be a state of drug satiety.”

Amending prior work

Some authors highlight work that might strengthen or refine interpretations. Others note how new or existing data might change conclusions.

With co-author Raphael Silberzahn, Eric Uhlmann documents their new work on names and career outcomes. They had previously reported, “Germans with noble-sounding surnames, such as Kaiser (“emperor”), König (“king”), and Fürst (“prince”), more frequently hold managerial positions…” Their new analysis seems to overturn their previous conclusions.

Like many researchers trying to identify new antitumor agents, Miguel Lopez-Lazaro and his colleagues began by testing compounds in a cancer cell line. Since publishing their work, they followed up in other cell lines. Now he considers whether these in vitro effects will really translate to therapeutic potential.

Teasing apart the functions of specific proteins in cells or animals can get complicated. Using inhibitors or genetic manipulation doesn’t always provide a clear picture.

For example, Jens Staal explored the interplay of the protease MALT1 and the deubiquitnase CYLD in immune cells. After further experiments, he updates his interpretation.

Meanwhile, Jim Woodgett notes that care should be taken with assigning specific functions to a single protein isoform. He highlights the trouble with glycogen synthase kinase-3 inhibitors. After a few comments on the subject, he remarks, “…no small molecule inhibitors are isoform selective – I am a scratched record.”

Bridging published updates

When substantive errors are found, updates are not always clearly connected to original publications. PubMed Commons gives authors a chance to link pieces together in PubMed.

Sometimes errors are reported in follow-up studies. Consider a mutation in an HIV protein that was correlated with survival. Stuart Ray notes that a subsequent report of an alignment error invalidates the findings.

Other times, flaws in methods or results lead to correction or retraction of a report.

Randy Blakely finds that a paper about the human dopamine transporter continues to be improperly cited, despite a correction to the results. He says, “I am hoping the PubMed Commons forum will provide a suitable opportunity to redirect readers attention to the, as yet, unknown properties of the E602G mutation…”

Ivan Oransky uses PubMed Commons to annotate recent retractions. He includes links with more about the history of the publication and why it was withdrawn. For instance, here he points to where co-blogger Adam Marcus notes, “Failure to cite leads to ignoble end for xenon paper, and a correction.”

If you’re an author of a PubMed-indexed publication and ready to get involved, check out this page to learn how you can get started.

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

Spotlight on… Amanda Capes-Davis, setting the cell line record straight

450755747You think you’ve found what you need – a cell model for a specific type of cancer you’re studying. But the label on those cells may have you fooled. In labs around the world, many cell lines are mistaken for characters they are not. Dr. Amanda Capes-Davis has seen it happen, time and again. She received her medical training and PhD in cancer genetics from the University of Sydney. After six years as a research officer at the Children’s Medical Research Institute (CMRI), she helped establish CellBank Australia, a non-profit cell line repository. Now working as a cell culture consultant and chair of the International Cell Line Authentication Committee (ICLAC), Capes-Davis is on a mission to bring the long-standing problem of cell line misidentification to light – and she’s using PubMed Commons as a tool in this fight.

Mistaken identities

Cell culture is a part of everyday life for many life science and biomedical researchers. To address biological questions, scientists often work with populations of cells grown in incubators. Typically, cells isolated from a human or other animal will only survive and multiply for a few days or weeks, even under optimal conditions. “Immortalized cell lines,” on the other hand, can be grown in flasks or dishes for months, even years. Often these lines are derived from cancers that allow cells to bypass checkpoints that would normally stop them from dividing.

The advent of immortalized cell culture 60 years ago opened doors for new studies, but there are also persistent problems. Many cell lines bear mistaken identities. So far, ICLAC has identified 472 cross-contaminated or misidentified cell lines, based on 89 publications. The cell type or tissue origin of cells grown is sometimes mislabeled at the outset. Other times, a cell line cross-contaminates another, overtaking the original line. “Perhaps 10-15% of all cell lines are cross-contaminated,” Capes-Davis reports.

HeLa cells exemplify the potential and the pitfalls of cell culture. Henrietta Lacks was a woman who unknowingly pushed biomedical science forward. While she was under treatment for aggressive cervical cancer, a sample of her tumor was taken. Shortly before her death in 1951, those cells were used to establish the first reported immortalized human cell line. Within a few years, the cells were widely used, including in development of the polio vaccine. However, HeLa cells grow so robustly that, if a few cells mistakenly get mixed in with another cell type, HeLa can quickly overtake the others. In their survey of the literature, ICLAC has noticed an abundance of HeLa contamination. Capes-Davis notes, “There are 135 different cell line contaminants, but HeLa is by far the commonest. We list 113 misidentified cell lines where HeLa is the contaminant.”

HeLa cross-contamination of cell lines was first reported in 1967. Yet many new publications continue to misidentify cross-contaminated cell lines. “It’s very understandable, I think, for a scientist,” Capes-Davis says. “You’re doing research in that field. You’re seeing everyone else using this cell line. You think this must be appropriate because all of your colleagues use it.” Reports of cross-contamination disappear under the mountain of other publications using the cell line. In doing as they were trained – building on work published by others – many scientists are actually perpetuating errors. Capes-Davis notes, “They say, research is meant to be self-correcting, but with these cell lines, that doesn’t appear to be the case.”

It’s impossible to fully assess the impact that cell line contamination has had – and continues to have – on research and development. “You only really get hints here or there,” Capes-Davis says. “I first learned about cell line contamination as a PhD student… The lab I was working in started to require testing as I was writing up my PhD.  That was quite a stressful experience for me – my PhD was entirely cell culture-based, and it was frightening to think that all my hard work might be wasted if those cell lines were contaminated.” In some cases, experimental results from misidentified cell lines supported patenting and testing of compounds in people. “These days, I think, with the level of regulation that comes in, problems with cross-contaminated cell lines will be picked up before an agent is trialed, but you have to wonder about the waste of time and waste of money required to get to that point.Amanda Capes-Davis

For Capes-Davis, though, solving cell line misidentification is about more than scientists’ time and research funding. “I am also a medical doctor and would go in to operating theatres to collect tissue samples from individuals who consented to their tissue being used in research.  Many cell lines represent a legacy from donors who have died as a result of that disease.  To me, testing of cell lines is part of our responsibility to the donor, and makes sure that we put the donor’s gift to the best use we can in finding future treatments.”

Correcting the record and the future course

In 2009, Capes-Davis joined two initiatives to address cell line misidentification. The American Type Culture Collection (ATCC) Standards Development Organization established a workgroup (ASN-0002) to develop standards for human cell line authentication. Capes-Davis recalls, “Some members wanted to have an ongoing group on cross-contamination.” During this time, she also collaborated with Ian Freshney to develop a database of cross-contaminated cell lines. “We could really see the value of having involvement of a larger group of people, the advantages of people being able to contribute data or having additional expert opinions on whether a cell line was cross-contaminated, whether or not it’s possible to find authentic stocks.” In 2012, she and other scientists  with a shared interest in the problem of cell line misidentification founded ICLAC.

“I think publicity and awareness is always a challenge. It’s always a bit of a surprise to people, even people who’ve been in the field a number of years,” Capes-Davis notes. “A lot of what we’re involved with is making people aware of the need for quality, even when they’re doing preclinical research. It’s not a series of steps that are going to be difficult to do, but it’s something that should be part of good lab practice. It’s part of good research.” ICLAC is also seeking to establish infrastructure for researchers, such as maintaining the database she and Freshney created, developing guidelines for best practices, and making resources available online.

Capes-Davis has taken to PubMed Commons to annotate publications that misreport identities of known cross-contaminated cell lines. “Ideally we want these things picked up as part of peer review, but it’s not as easy sometimes as you might think,” she notes. “Correcting the scientific record is a really important thing because even if you take the assumption that a signaling pathway isn’t going to be affected, that’s not necessarily going to be the case for another paper that cites that work. The assumption is that if you describe a cell line as oral carcinoma, that’s what it is. It might not matter for one person’s work, but it could well matter for the person who reads that paper.”

“I use PubMed pretty much everyday… it’s an area where a lot of people come to look at abstracts and hunt down papers,” Capes-Davis notes. “So [PubMed Commons] seemed like a great opportunity to raise awareness of our database… We’re hoping that if we do the best we can to bring all the known publications that relate to cross-contaminated cell lines into our database, that will be a useful resource for people. It’s not enough…but it’s certainly a step in the right direction.”

Learn more about PubMed Commons. If you’re an author in PubMed, join and make your own contribution to scientific discourse.



Blogs and their links with PubMed Commons

Photo of blog entry in a dictionary

Blogs grew quickly into a dynamic and substantial element in the way we discuss, criticize and share information about scientific publications. Science blogs are one of the filters many now use for the science literature – and one of the ways members of the public learn about research results and efforts.

Anchoring these blog posts to the publications they discuss is one of the ways members are putting PubMed Commons to good use. Here are examples from the spectrum covered by dozens of links to blog posts so far in the Commons.

Dorothy Bishop responded to Michael Farthing’s lecture on the challenge of research conduct, including links to her blog posts on perverse incentives for academics and registering proposed research in psychology.

Daniel Simons writes post-publication peer reviews on his blog. He’s posted one on Joaquin Anguera and colleagues’ study of video game training for cognitive control,  and one on a recent study of inattentional blindness to African Americans by Jazmin Brown-Iannuzzi at the Commons.

Coming across a media report of a study draws the attention of many academic bloggers, spurring both posts on their blogs and links to them on PubMed Commons. This happened when Andrew Kniss saw a newspaper article on Carsten Bruehl’s conclusions about pesticide use and frog population decline.

In other areas where there’s a lot of debate about a publication, or they read a post they found helpful, Commons members draw readers’ attention to detailed coverage in another person’s blog. George McNamara, for example, points to a post by Michael Eisen at the PubMed record for John Bohannon’s publication about peer review at open-access journals.

Important blog posts also unwrap the history of misleading use of studies in public debates. An example now in the Commons is about an autism prevalence study by Simon Baron-Cohen and colleagues. It was added by Jamie Horder, pointing to Ben Goldacre’s post on “The story behind this paper, and the remarkable media coverage it received.” It’s a Whodunit? about an MMR vaccine scare in the media.

Retractions of articles are being noted with links to blog posts about the background, for example by Allison Stelling and Ivan Oransky.

Attacks on research lead defenders to their blogs, too – and now to the Commons afterwards. James Coyne responded to critics of a randomized trial by William Hollingworth and colleagues of screening for distress in cancer patients.

Authors of publications who discuss their work on their own blogs draw readers’ attention to these posts at PubMed Commons. For example, Anne-Marie Cunningham has posted links to blog posts on her work with colleagues incorporating a pre-publication version with one article and an audio-visual presentation with another.

Seth Borderstein links to a post explaining the background to a publication on maternal microbe transmission. And Jonathan Eisen links to his post telling the story behind his team’s work on phylogenetic trees.

Discussing implications for future research of a study’s findings are another part of blog posts brought into the Commons. Graham Coop posted a link to his blog post on Sriram Sankararaman and colleagues’ work on genetic variants on the possible offspring of Neandertal and modern human parents.

The Commons is growing: from 2,000 members in January to over 3,000 today, who have made just over 1,000 comments so far. Want to keep up with comments that are getting good ranking scores in PubMed Commons? We tweet them @PubMedCommons.

That’s one more important reason for PubMed Commons members to add their “helpful? yes or no” clicks to the system: when you read it, please rate it. Help shape the Commons into a valuable place for discussions about biomedical publications – and drawing together the valuable discussions from outside. If you write or read a blog with a valuable discussion about a publication, think about sharing it at PubMed Commons.

The PubMed Commons team

More information

Membership of PubMed Commons is open to all authors in PubMed.

Join PubMed Commons

“You found this helpful:” What people like in comments on PubMed

Comment search and alert: A PubMed Commons guide