Critiquing systematic review search strategies on PubMed

More than 1.1 million publications were indexed in PubMed in 2016, bringing the total number of PubMed records to more than 27 million. It’s no wonder that systematic reviews have become popular (currently there are more than 40,000 systematic reviews in PubMed Health alone). Systematic reviews and related methods aim to pull together all relevant studies on a defined topic and synthesize the evidence to evaluate what’s known. The approach has been used to inform clinical research and practice for decades, and its use is spreading.

As with any research, systematic reviews are only as good as their methods. A critical method here is literature searching. Some librarians and information specialists have taken to PubMed Commons to tackle issues surrounding the quality and efficacy of search strategies and their reporting. They also hope to raise awareness of librarians’ expertise in this area. We interviewed 5 librarians to learn more about their perspectives and how they’re using PubMed Commons.

 

Designing and reporting for reproducibility

Melissa Rethlefsen2

Melissa Rethlefsen

Melissa Rethlefsen is deputy director of the Eccles Health Sciences Library at University of Utah and section director of the Systematic Review Core, which is integrated with the Center for Clinical and Translational Science. She has been investigating the quality of reported systematic review search strategies. She and colleagues at Mayo Clinic found that systematic reviews that included librarians as co-authors were more likely to meet standards such as those recommended by the Institute of Medicine. “It really does benefit you to have an information specialist or librarian on your team,” Rethlefsen says.

“Just like any other type of research, your method should be described clearly enough that it can be reproduced. We see so many systematic reviews that are published without this really critical information, and then it’s really hard to assess their quality,” Rethlefsen notes.

A number of journals have endorsed the use of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Michelle Fiander, a systematic review librarian at the University of Utah, says, “PRISMA tells you what to say, what to report, the types of information that should be there. But they don’t tell you how.”

Mary Klem, a research and instruction librarian in the Health Sciences Library System at the University of Pittsburgh, has noticed the disconnect between statements concerning PRISMA and actual implementation. “In the article I commented on, the authors’ primary rationale for completing their review was that a prior review on the topic had not used a systematic or well-defined search strategy,” she shares. “I thought it was awesome that someone had critiqued a review like that! So I was disappointed to see that the documentation and searches in this new improved review weren’t thorough or comprehensive, and felt like I needed to note that.”

 

Putting expertise forward

Some librarians have used PubMed Commons because it’s visible, it’s fast, and they see potential for the impact to extend beyond a single publication.

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Donna Berryman

“In a practical sense, using PubMed Commons seemed to be a better choice than writing a letter to the editor because of its immediacy and visibility,” Donna Berryman, the director of the Miner Libraries in the Institute for Innovative Education at the University of Rochester Medical Center, says. “Many, many people will find the article I commented on by doing a search in PubMed. If they look at the record for the article, my comment will be there. I’m not sure how many people would even look at a letter to the editor. In addition, there’s always a chance the letter won’t get published, and, if it does, there’s generally a long gap between when an article appears in a journal and when the letter to the editor might appear. All of those things argue against visibility. So, PubMed Commons gives my words visibility and immediacy.”

Wichor Bramer also favors the transparency and timeliness of PubMed Commons. He is a biomedical information specialist at Erasmus University Medical Center in the Netherlands, where he’s also currently working on his PhD on search methodologies for systematic reviews. He shares, “My last comment was on the details of a search strategy. Julie Glanville, who’s a famous searcher for reviews, responded to that, so you can communicate publicly with the authors.” Author responses can create a “vivid discussion that’s available for anyone to see.”

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Michelle Fiander

Bramer is also finding value as an author himself. He notes that he’s used comments on his first article comparing PubMed and Google Scholar to change the way he did some things for his second article. “The comments that we get help me create better articles in the future.”

For Fiander, PubMed Commons offers an opportunity to “get my voice out there and point out things. Maybe it will end up stirring some better standards among journal editors. If you have a paper and you’re indexed in there, you can comment. It’s easier than writing a letter to the editor. I think the freedom of it is good.”

 

Commenting with care

But freedom doesn’t mean off the cuff for these commenters. “I tend to read my comment, be careful that I’m being accurate, that I’m not overstating or saying something that’s inaccurate,” Fiander notes.

Berryman has commented once but suspects she will comment again. “PubMed Commons strikes me as a place to have reasoned, deliberate comments. It’s not like commenting on Facebook or Twitter. So, one thing I always think about is whether I can write my comment in a way that is constructive and will add to the body of knowledge – and that takes both thought and time.”

I see it as post-publication peer review,” Bramer says. “I first create it. I don’t post it immediately. I put it away for maybe a day and look at it the next day and see different things, see if I can improve some things.”

Rethlefsen understands that commenting on PubMed, especially the first time, isn’t necessarily easy. “It’s not really a space where librarians had actively engaged before. Irreproducible search strategies were always a thing that librarians talked to each other about.” But she had concerns about what looked like, on the face of it, an excellent search strategy that she couldn’t reproduce. So she decided to go to PubMed Commons. “I worked on it, I deleted it, I re-wrote it, and I deleted it. And finally I pushed the publish button. It was intimidating because I’d never done it before. But once I got the reaction that I did [from colleagues and the librarian community], it became really clear to me that this was a more important space than I’d thought before.”

 

Joining in

Feeling inspired? If you have a publication indexed in PubMed, then you’re eligible to join PubMed Commons and start commenting! Learn more about getting started with PubMed Commons.

PubMed Commons stats through March 31, 2017. Members: 10962 joined, 1637 commented. Comments: 6372 comments posted to 5078 publications.

Authors alerting readers via PubMed Commons

Journals can issue correction and errata notices to notify readers of errors and, as necessary, revise text and data in publications. Yet these processes can take time. Authors sometimes encounter obstacles to publishing corrections. Some authors use PubMed Commons to alert readers to issues or to refine language and interpretations. Correcting the record via journal notices is important, and it’s great to see authors add speed and transparency with post-publication updates.

corr2Earlier this year, Garret Stuber commented on a publication on hormonal control in social reward. In the days after it appeared in press, some errors came to his attention, which he was working to address through a formal correction notice. Stuber told Retraction Watch that, in the meantime, he commented “in an effort for immediate notice and transparency to what occurred.”

Sometimes an error may significantly change the results of a study. Stefan Hofmann commented on a meta-analysis he co-authored, examining the effects of oxytocin on an array of psychiatric symptoms. However, readers raised some points, prompting another look at the data. Errors were made in specifying the direction of outcomes investigated. Hofmann reported the re-calculated effect sizes and indicated that the article is being retracted.

Here are some more authors setting this great example:

Journal corrections revise the version of record for a publication, and PubMed Commons does not replace that. But it does offer another way for authors to provide clarifications, point to interim and published corrections, and alert readers to errors quickly. And it’s good to see authors taking advantage of PubMed Commons to pass that information along to the community.

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

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