Is PubMed Hurting Scientific Journals?

A study concludes that the open access repository is decreasing biomedical journal readership.

By Kate Yandell | April 5, 2013

WIKIMEDIA, TOBIAS M. ECKRICHIn 2008 the National Institutes of Health (NIH) began mandating that all of the research the agency funded be publicly available within a year and deposited in the online repository PubMed Central (PMC). Now PMC is taking away traffic from journal websites, according to a new study published in The FASEB Journal, even when the journals also provide the articles for free.

The paper’s author, Philip Davis, who runs his own consulting company in Ithaca, New York, did a case-control study, analyzing PDF and HTML article downloads taking place between February 2008 and January 2011 from 14 biomedical research journals. He compared “cases”—NIH-funded articles that became free both on PMC and on the journal websites—with “controls”—articles not funded by the NIH, which the journals made freely available after a year on their website but did not post to PMC—and found that articles posted on PMC received 21.4 percent fewer HTML downloads from the journal websites than the articles not available on PMC, and 13.8 percent fewer PDF downloads

The NIH’s open access policy has been hailed as one that gives taxpayers access to research they have paid for, but Davis argues that PMC is having a negative effect on scientific societies’ cohesion by drawing traffic away from their websites. Readers who download articles from PMC will not see society announcements or other contextual information the journal provides, he said.

“I hope that studies like these will help inform the public debate on the effects of open government literature repositories on various stakeholders and aid in the formation of evidence-based public policy,” Davis told Science 2.0

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Avatar of: Casey Bergman

Casey Bergman

Posts: 2

April 5, 2013

I have several comments on this piece that readers of The Scientist should be aware of:

First, the title of your piece is misleading and incorrectly characterizes the point of Davis' article. Davis claims that PubMed Central, not PubMed, is taking a share of the traffic that would otherwise go to publisher websites.  Pubmed is the searchable database of abstracts for papers indexed by MEDLINE, and is the principal search engine (along with Google Scholar) for most scientists to find relevant papers and access the full text of biomedical literature, either at publisher websites or PubMed Central. Thus, it is absurd to claim that PubMed hurts scientific journals.

Second, as stated in the paper, this study was was "supported by" the American Physiological Society (APS), which is a member of Federation of American Societies for Experimental Biology (FASEB), which publishes FASEB Journal, the journal in which this paper was published.  As the author is a private consultant who declares APS as one of his clients (, one can only assume that APS played a role in the funding of this study. Unfortunately, this conflict of interest is not declared in the paper, and this oversight is in contradiction of the policies of FASEB Journal ( This potential conflict of interest is doubly concerning because the articles studied in this paper are actually from the FASEB Journal and several other journals published by the APS (e.g. American Journal of Physiology—Cell Physiology, American Journal of Physiology—Endocrinology and Metabolism, etc.)

Third, while Davis asserts that research such as his should form the basis of "evidence-based public policy", it is worth noting that the underlying datasets that forms the basis of his conclusions are not provided as supplementary materials to the paper.  The lack of availability these datasets makes it difficult, if not impossible, for any other researcher to replicate Davis' findings or identify any biases or flaws in his assumptions or analyses. Making raw data available at the time of publication is increasingly considered standard practice in online publishing, so it is worth questioning why these datasets have not been made publicly available in this case. If public policy is to be informed by evidence, surely the fundamental evidence (not just summary evidence), should be made available for scrutiny to inform debate.

Fourth, it is perhaps more than a little ironic that the paper in question is available under an immediate Open Access model.  If PubMed Central's goals of making the scientific literature openly accessible is so harmful to the web traffic scientific publishers, it seems that the manner in which this article was published may contradict the intended message of the study.

Avatar of: Jim Woodgett

Jim Woodgett

Posts: 1

April 5, 2013

Echoing Casey Bergman's comments, the advent of the internet has turned the publishing model upside down. When scientists published their work in paper form and accessed it through libraries and personal subscriptions, the business model (be it scientific society or fully commercial publisher) allowed for the "excess" of delivery of information that the scientist did not necessarily or usually desire. The advent of the web has had a similar if not even more extreme effect to iTunes/mp3s on album sales. Researchers can directly find and access the precise content they want with nary a peek at the virtual pages surrounding that document, nevermind the actual TOC. Expecting this practice to change is a sure way to obsolescence unless value is added to the journal outside of its original publications of manuscripts. Such value-add may be links to commentries, editorials, other papers, etc. that are RELEVANT to the landing article that the surfing scientist initially accessed. Attempts to obfuscate the process by interjecting between the query and the result will simply turn off the inquisitor and result in even more reliance/preference on repositories such as PMC. Instead of complaining about or trying to kill iTunes/PMC, it is incumbent on the publishers to find ways to add value to their own repositories.

The business test here is what the consumer (the scientist) wants. PMC isn't going away. Publishers need to adapt to this reality to survive.

Avatar of: Richard Sever

Richard Sever

Posts: 2

April 7, 2013

PMC isn't going away and nor should it. However, it should develop on a course that provides real utility to scientists, in particular text miners. Unfortunately, it has abandoned functionality that would have achieved this, in favor of developing features that many perceive as redundant.

PMC used to offer a feature called Publink, in which publishers made available all content for searching – on the condition that search results linked back to papers on journal websites rather than PMC copies of these papers. This strategy essentially created a dark archive behind PubMed (the interface where most searches actually take place) that had the potential to create a full-text archive of the entire literature that would have been invaluable to text miners – and almost impossible for publishers to justify opposing.

The Publink functionality was abandoned several years ago and instead PMC has taken a trajectory aimed at displaying content. This has embroiled it in the green-vs-gold OA debate and made content release subject to embargos. Most importantly for scientists it has meant that it has become an incomplete archive. We should ask why this course was chosen, what PMC’s mission is, and if a new mandate based around Publink could achieve this most effectively.

Avatar of: Phil Davis

Phil Davis

Posts: 1

April 7, 2013

Personal attacks are the weakest, last resort of individuals who have little else to contribute to a scientific debate, as is the list of suspicious and disingenuous statements by Casey Bergman. I offered Mr. Bergman an anonymized copy of the dataset for verification purposes--a fact unmentioned in his litany--however these conditions were simply unacceptable to him. A closer reading of the article lists my employment status right below my name and a statement of financial support at the end of the paper, along with the following declaration of roles and responsibilities:

"The author was solely responsible for the design and conduct of the study, collection and management of the data, data analysis and interpretation, preparation and submission of the manuscript, and can take responsibility for the integrity of the data and accuracy of the analysis."

I hope readers will consider the article on its own merits rather than being contingent upon the social and employment status of its author. University professors are not the only ones who reserve the right to conduct science.

Avatar of: Casey Bergman

Casey Bergman

Posts: 2

April 14, 2013

Apologies Phil if you felt that these comments were personal in any way; this was not my intent. My aim was to correct errors in The Scientist's coverage and alert readers to possible conflicts of interest that are not immediately apparent in the primary article or The Scientist's piece.  

Regarding the availability of the dataset in this study, it is a fact that it was not made available at the time of publication. It is true that I did not make our private correspondence public, since I would have assumed you would view this as a breach of confidence without first asking for your permission to quote you.  But as you have chosen to make this exchange public, I will note for the record that you refused to provide a dataset that included DOIs of the papers in this study, because of restrictions on data sharing imposed by the publishers (some of whom are also funders) that gave you access to data. The reason this restriction is important is that no scientist can match download statistics in your anonymized dataset back to the original papers to investigate underlying biases and confounding factors in the "control" and "PMC" sets (e.g. research topic), which may explain your results.  

This refusal to make data available for extension and deeper investigation, not merely statistical replication, is of course not a requirement of FASEB J or other journals. Many scientists do not share their data openly, especially when funded by private industry. What is of concern in this case is that the funder of the study, the APS, is also the parent organization of one of the main publishers that both provided data and imposed data sharing restrictions.  Moreover, the funders and data providers are also members of FASEB, which publishes the journal in which this study was reported. Given that the main message of the study is that publishers are being "hurt" by PubMed Central, there appear to be several conflicts of interest here regarding society publishers funding, providing data, preventing this data from being openly investigated, and ultimately publishing the study at hand.

Let's be clear here: we are not dealing with sensitive medical or other personal data here, we are dealing with download statistics from journal articles, information that many journals actively give away for free on their websites. I can see no reason that download statistics linked to DOIs cannot be made available for further analysis, other than to impede other scientists from investigating the claims of this study more fully.

Let me also clarify that I have no issue with privately-funded research and research conducted at non-academic institutions being published in academic journals. I fully agree that everyone has a right to practice science, not just those in the ivory tower. My concern here has nothing to do with you affiliation. It has everything to do with real and/or apparent conflicts of interest. I would have the same concerns about any study that was funded by a by a private entity using data provided by that entity, which was not made publicly available for scrutiny, regardless of their affiliation.

Finally, regarding your declaration of possible conflict of interests, according to the FASEB J's guideline (, authors are required to explicitly disclose conflicts of interest in the acknowledgements: "If the article is accepted for publication, information on the potential conflict of interest will be included in the acknowledgments section of the article." Unfortunately, the potential conflicts of interest in this case were not made explicit, and your disclaimer in the paper excerpted above only relates to responsibility of the data/analysis, which is a minimal standard expected for all scientists and does not reveal the nature of the issues at hand. A full disclosure of potential conflicts of interest in this case would have stated something like: "This study was funded by the APS, who provided access to data in the study, and is a member of FASEB who publishes the FASEB J."  This sort of clear, direct conflict of interest statement would be an absolute requirement, for example, in a study on the effects of a drug funded by a pharmaceutical company using data from a private research lab. I see no difference in this case.

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