PubMed Central (PMC) says it’s not a publisher. PubMed claims to have a fair process that it applies uniformly to include journals in its index. And as a government agency, PMC is generally prohibited from competing with one or more thriving private industries.

Yet, last week, with a set of actions around the fledgling funder-backed journal eLife, it became clear that PMC is a publisher, that PubMed’s process for indexing journals is not uniformly or fairly applied and can be exploited, and that PMC competes with both publishers and publishing technology companies, leveraging PubMed itself in these competitions.

dirty pool
Dirty pool (pun intended).

Let’s break this down claim by claim.

PubMed Central As Publisher

PMC states definitively on its site that it is not a publisher:

PMC, itself, is not a publisher.

What is a publisher? An entity which engages in:

. . . the activity of making information available to general public.

PubMed has long been a publisher of abstracts. PMC is clearly a publisher of full-text content. Therefore, their contention that PMC is not a publisher is simply wrong.

However, there are degrees of publishing — secondary, embargoed publication is qualitatively different than primary, immediate publication. A downstream publisher is different from a primary publisher. PMC is widely understood to be a secondary, embargoed publisher.

But what if it’s becoming a primary publisher?

PMC and PubMed require publishers to establish independent editorial and publishing practices and have these reviewed and evaluated after they’ve been in effect for some time. This is how it’s described in PubMed and PMC documentation, and this what the community generally believes to be true and adheres to. For instance, getting content into PMC requires publishers to meet both technical and scientific standards, including:

The journal must have a reasonable number of published articles in order for NLM to make a decision about its scientific quality.

A journal will be deemed to be eligible for inclusion in PMC if the NLM Selection and Acquisition Section determines that it conforms to the scientific quality criteria specified in the Collection Development Manual of the National Library of Medicine.

In standard communications with publishers about these protocols, the NLM and PubMed state:

A journal needs to be included in the NLM Collection to meet PMC’s scientific quality standard. This review can take place once [the title] has published 15 articles.

So, a journal has to publish 15 articles before any review can take place.

But what would it mean if a journal’s first articles were published on PMC, and only on PMC? No review process could have occurred. There would have been no independent publication practices established, and therefore nothing to review. Allowing articles into PMC otherwise would be an abrogation of standards, or something equally questionable. It would be even more of a violation of stated policy if fewer than 15 articles were involved.

Last week, eLife published its first papers — four research articles, four commentaries, and an editorial. That’s a total of nine articles, short of the 15 required, and the minority are scientific reports. Yet, where did eLife publish them? On, their domain? On HighWire Press, where its publisher site is being built? No. It published them on PubMed Central. All URLs listed on the eLife site point to this US government Web site ( In a comment on this blog last week, Robert Kiley of Wellcome Trust pointed to the only published version of eLife’s introductory editorial — which resides on PMC. The US government is acting as the online publisher of eLife.

eLife branding is prominently displayed. Within the eLife logo, the four links work separately and well. This was not a sloppy job, but a careful integration. This required coordination and planning between eLife and PMC. PMC was clearly acting as an extension of eLife.

Screen shot of how eLife looks on PMC.

eLife put a statement on its site about how PMC was publishing its articles:

To avoid unnecessary delays in making the first accepted articles available, we are listing articles that are ready for publication here and publishing the articles themselves on PubMed Central (PMC), the public archive for life and biomedical science literature at the US National Library of Medicine. Additional papers will be published this fall and, as planned, we will launch eLife’s journal Web site this Winter.

“Unnecessary delays” would be those we all tolerate as independent publishers in our dealings with PubMed and PMC — waiting for our hosting platform to be ready, proving our independent ability to publish by abiding by the timeframe, article count, and technical requirements of PubMed or PMC, and so forth. eLife editors are being disingenuous by saying these things are “unnecessary.” They are required, and they are the norm. The are only “unnecessary” if someone helps you short-circuit the process.

The agency of the statement is also interesting — “we” (meaning eLife) are publishing the articles themselves on PMC. This assignment of agency to eLife makes it seem that PMC had no choice in the matter, and that the US government, through the NLM and NCBI, is merely a publicly available and free publishing platform, ala WordPress.

Where was the review? Where were the standards? Where was the process?

I spoke with David Lipman of NCBI about this. He told me that eLife submitted a PMC application following what he termed “the regular procedure.” During the application process, eLife’s representatives mentioned that their site was not up. A discussion ensued, the details of which he claimed to know nothing about, and the powers that be at PMC or NLM agreed to publish the eLife articles on PMC before the normal requirements had been met, and before eLife had demonstrated any independent ability to publish. I asked him if the NLM Acquisition and Selection Section had approved the application. He said they had. I tried to contact Joyce Backus, the head of the Section, over the weekend prior to the publication of this post, but we weren’t able to connect. If warranted, I’ll write more about the questions I asked her later.

Lipman claimed that eLife “seemed like a reasonable bet” owing to the quality of its backers and its editorial staff. Yet, when asked why a publisher like AAAS or the American Chemical Society or Lippincott or a hundred others don’t benefit from the same affordances and don’t by extension seem like “a reasonable bet,” he had no good answer.

Clearly, PMC is the primary publisher of eLife. Articles in eLife appear nowhere else — not in print, not on a publishing platform through independent private means, nowhere. The editors of eLife are representing that it was their doing, but that’s clearly not true — they needed agreement and assistance from PMC, which is owned by an agency of the US government.

The implications of this are troubling. US taxpayers are now directly subsidizing a Delaware-based 501(c)3 that is also partially a UK-based charity. NLM, PMC, and NCBI have given one entity special accommodation and violated its own policies and practices to make this happen.

As if this weren’t enough, PMC’s role as a primary publisher doesn’t stop with eLife. The online version of the Journal of the Medical Library Association (JMLA) is also published primarily on PMC. PMC also publishes the Journal of Biomolecular Techniques for the Association of Biomolecular Resource Facilities (ABRF). The PMC site for this journal is framed in the ABRF site.

In much the same way that any commercial or non-profit publisher is the publisher of a society’s journal, PMC is a primary publisher — for eLife, and for at least two other journals.

PubMed’s Indexing Process Can Be Subverted

eLife published its first articles on October 15, 2012 — one week ago. Yet, search PubMed, and lo and behold, eLife articles are included in PubMed. The record in the NLM Catalog still states “PubMed Coverage to be announced” and “Not currently indexed for MEDLINE.” This distinction is functionally meaningless to our readers, authors, and most of our editors. PubMed is what they use, and PubMed is where they want to be indexed. So it’s no surprise that PubMed is what is being leveraged by PMC.

The confusion between PubMed and MEDLINE, along with how PMC can be used as a backdoor into PubMed, is what eLife is exploiting, with the help of having PMC as its primary publisher.

It takes more to get into MEDLINE. In the Collection Development Manual, the following statement appears:

Once an electronic journal has been accessible for at least six months, an editor or publisher may request that the journal be reviewed for possible indexing if at least 20 articles have been published and made available online.

This statement has a few aspects. The electronic journal must be accessible for at least six months — independently. Not published on PMC, but accessible through private means as evidence that it is sustainable and independent. For six months — not six hours or six minutes. By having PMC as its primary publisher, eLife is subverting these requirements. They are not likely to launch as an independent journal — independent of US government publishing operations, that is — until early next year.

My organization began publishing two online-only journals more than a year ago. We followed the stated requirements, which are reiterated on the application itself. We waited six months and 20 articles before submitting out applications, even a little longer to ensure that some technical issues could be worked out and some editorial roles assigned after the journals were launched. We are still waiting to be indexed in PubMed and MEDLINE. We followed the process. Dozens and dozens of other publishers do so, as well.

Being indexed in PubMed is a big deal for fledgling journals, because editors, authors, and readers often mistake PubMed for MEDLINE. Indexing in PubMed makes a difference in attracting editors, it makes a difference in attracting good papers, and it makes a difference in establishing legitimacy with an audience. Allowing certain journals to shortcut their way into PubMed in direct violation of its own stated processes and requirements is just wrong, but to leverage this to move the needle for PMC only compounds the problem. And to allow a new publisher to leverage PMC as eLife has goes one step further.

There was no one- to two-year wait for eLife to get into PubMed through MEDLINE because they got in immediately by being in PMC. No process akin to what other publishers have to go through. Immediate acceptance into PubMed. Magically. Inexplicably. With the US government as its primary publisher.

Before I spoke with him, I emailed Lipman, head of NCBI, last week to get his perspective on this. Here’s what he said:

The NLM Selection and Acquisition Section considers a number of factors in deciding whether the scientific quality of a journal merits acceptance into PMC. The minimum number of articles required for this evaluation may vary based on the credentials of the publisher and/or sponsoring organization and of the editorial board, and on the quality of the journal’s editorial policies and practices. eLife citations appear in PubMed after the articles are released in PMC, which is no different from any other non-Medline journal in PMC.

In my conversation with him a couple of days later, Lipman referred again and again back to this email, as if it explained everything. Yet, when I quoted the NLM’s own stated standards back to him, the pregnant pause was notable. And, as mentioned above, he couldn’t explain why the “practices” and “policies” and “credentials” of eLife might be stronger than those of a hundred other, more established publishers.

A matter of minutes after I received Lipman’s email quoted above, another publisher I was speaking with received a response from PMC to a general question about their policies and approach, to see if being open access (OA) made a difference to the process:

One of your new journals (it doesn’t matter if it is OA or not) will need to publish at least 15 articles before it can be evaluated by the Selections Group. Once it is approved by the Selections Group, then sample articles can be sent to PMC for data evaluation. When you’re ready to submit a new journal, please just send me the title, ISSN(s), and url.

So, again we have the 15-article requirement — for everyone, it seems, except eLife.

Lipman’s response is coded and disingenuous because he says that things like “credentials,” “policies,” and “practices” inform their decisions about what gets this magical treatment, but obviously the process as understood by people who work with the Selections Group is not the process Lipman or someone else he knows uses.

As I mentioned above, I asked him about this in our phone call. There was not a satisfactory answer. He said grand things like “we look at the big picture” and “we’ve been burned by publishers who have moved or stopped journals” (how moving a journal affects PubMed is beyond me), and “it seemed like a reasonable bet” to take eLife early.

Let’s take his words at face value — would any traditional publisher lack in “credentials” or “policies” or “practices” around a new journal and quality? Not very likely. In fact, if quality and reliability were the criteria guiding decision-making — and you might hope they would be — you’d expect a fast lane for established publishers, many of which have been around for more than a century, attract top-tier editors, and have advanced publishing infrastructure. How a journal like eLife — which hasn’t proven it can publish independently of US government subsidy, which hasn’t published the requisite number of articles, and which has yet to demonstrate solid editorial or business practices — gets a free pass suggests a strong ulterior motive is at work, something that may approach outright cronyism.

Lipman’s criteria are at worst euphemisms for a specific set of policies and practices, perhaps OA, as some people I spoke with suspect — yet, even other OA publishers don’t get this magic. They have to wait, follow procedures, and prove they can publish independently. So this exception was even more specific — it was for eLife, and that’s very troubling.

In addition to being unfair and infuriating, this event also shows how PMC is part of the competitive landscape with a definite role in determining who wins and loses. It leverages PubMed in this regard. It takes an active and biased role in who benefits and who suffers. It is competitive. And this is our next topic.

PubMed Central Competes With Publishers and Technology Companies

Thomas Jefferson stated that, “The legitimate powers of government extend to such acts only as are injurious to others.” This generally informs the distinction between government regulation versus government competition. Otherwise, a more laissez-faire approach is followed, and government agencies competing with private enterprise is clearly discouraged. In 2011, the Computer and Communication Industry Association (CCIA), in objecting to the potential for the IRS to enter the market for electronic tax returns preparation software, competing with TurboTax and its equivalents, wrote:

While we support government efforts to modernize operations, improve taxpayer services and utilize the tools and technologies of the Information Age, we cannot support the government as a competitor in commercial markets. Such activity is antithetical to a successful free market and unfair to American taxpayers and shareholders of private businesses, who are forced to compete with publicly-funded government entities. Simply put, the U.S. Government exists to perform essential functions for its citizens. Launching commercial enterprises is not one of them.

Concerns over government competition with private enterprise permeate many legislative actions, and are foundational to a democracy that emerged from a domineering ruling government. In the case of PMC, we have to recall that “free” is a price in the commercial market — one that makes PMC competitive both with publishers and with technology companies.

PubMed Central Competes with Publishers for Traffic. A recent analysis showed that deposit in PMC by physiology journals decreased traffic to the publishers Web property by 14%. Traffic is the lifeblood of online publications. It allows publishers to sell advertising, show off related content, establish their brand, communicate with potential authors, track their success, sell site licenses, and measure editorial initiatives. PMC competes with all of this by maintaining a redundant set of articles which draws traffic away from the main publisher sites. PMC also makes PMC “free article” links more prominent in search results than similar publisher links, another obvious ploy to compete with publishers for traffic and brand prominence.

PMC Leverages PubMed to Tilt the Playing Field Unfairly. The issue noted above — favoritism within PMC and PubMed for publishers that conduct business in a way the leadership there must privately approve — creates competitive advantages for publishers of a certain type. That is, certain OA publishers are allowed to be indexed immediately in PubMed, skipping that messy and dicey period other publishers must endure and overcome, during which time authors and editors are a little uncertain of the new initiative and rely on the reputation of the publisher and other editors for sustenance. By getting indexed faster — immediately, in fact — eLife unfairly leapfrogs other journals that are doing it properly, by the rules, and according to published protocols. This gives eLife a competitive advantage with authors and editors (who immediately have a PubMed-indexed journal to edit and publish in), thereby creating a competitive disadvantage for others. There isn’t a level playing field.

NCBI Competes with Technology Companies. PMC is also competing with technology companies. By publishing JMLA and JBT, PMC is taking potential business away from HighWire Press, Atypon, Silverchair, Publishing Technology, or a number of other potential technology providers. Other OA library journals, such as College & Research Libraries (CR&L), pay for commercial hosting, as they should. There is no reason for the government to be providing free technology to JMLA or JBT. The same goes for eLife. By publishing eLife before the HighWire Press installation for eLife is complete, PMC is providing an unfair market advantage to eLife but also competing with HighWire Press — perhaps eLife will find the PMC solution satisfactory and cut short its efforts at HighWire. The US government shouldn’t be providing them with an alternative to a signed contract, nor should it be removing journals like JMLA and JBT from the technology marketplace.

It’s no secret that PMC has been competing with traditional publishers for a long time, and is becoming more competitive with each passing year. From quashing of the PubLink proposal years ago — wherein PMC would have been a dark archive and all free papers would have resided on publisher sites — to the relative suppression of publisher links in deference to PMC links on PubMed search results, the leadership and governance at NCBI, PubMed, and PubMed Central has been conducting a campaign of favoritism for certain OA publishers and for OA in general while competing with traditional publishers. And if this weren’t bad enough, PMC is also competing with the publishing technology industry by taking potential customers off the market and subsidizing their publication efforts with taxpayer funds.

Close Ties Between PMC and eLife

As I mentioned above, the special treatment afforded eLife seems to approach cronyism, which is defined as “partiality to long-standing friends, especially by appointing them to positions of authority, regardless of their qualifications.” So it’s not surprising that there are relationships between eLife and PMC. For instance, a member of the eLife Board of Directors, Elizabeth Marincola, served on the original PMC National Advisory Committee (NAC) from 2000-2003. Currently, Christopher Bird, the Solicitor for the Wellcome Trust — a major funder behind eLifeserves on the PMC NAC.

These ties are worth noting. Given the exceptional treatment eLife has received, these relationships do not appear to be innocuous.

As I’ve noted elsewhere, eLife is skirting some major reputational issues, eliding them in hopes nobody notices — issues such as the conflict of interests inherent in funders acting as publishers. In addition, the editor-in-chief is funded by HHMI, one of the funders of eLife, and the two deputy editors are funded by Wellcome Trust (Watt) and Max Plack (Weigel), the other two funders of eLife. There is no unbroken line between funders and eLife’s top editorial decision-makers, making this journal a real insiders’ game.

eLife’s first approach to get its materials out has been to subvert rules and standards through insider dealing and cronyism. This is not a good sign for their alleged neutrality and fairness going forward, and suggests that their ability to manage conflicting interests is less robust than imagined. The proponents of eLife have told its critics to wait and see what eLife does before judging it. We’ve seen a few things now. They are not reassuring.

So it seems PMC — by taking a “reasonable bet” in violation of its own policies — is now an odds-maker cooperating inappropriately with at least one customer by using a stacked deck and, by becoming the primary publisher of eLife, dealing from the bottom of the deck. No wonder the “bet” seemed “reasonable.” PMC controls the odds.


Last week, we saw a set of problematic and untoward activities come to full light as PMC became the primary publisher of eLife content in violation of its own stated policies — policies its own staff reiterated just last week via email to another publisher. These problems include:

  • Breaking its self-definition of not being a publisher, by becoming the primary and sole publisher of eLife
  • Breaking its own stated policies and practices for inclusion in PMC, and therefore PubMed
  • Leveraging PubMed indexing in a more general sense to reward certain publishers PMC leadership favors
  • Making exceptions and granting waivers without explanation
  • Competing with both publishers for traffic by manipulating PubMed to favor PMC articles and by hosting redundant versions of published content
  • Competing with publishing technology companies by taking customers off the market and undercutting contracts currently in place

In total, these practices and policies raise many questions about how PMC is managed, how PMC is spending its $1-3 million budget, how PubMed works and is being used by those in a position of authority, and whether the NLM is managing the evolution of online publishing in fair, objective, even-handed, and trustworthy manner.

Bottom Line

PMC needs to play by its own rules, and apply them objectively and uniformly. It should not say one thing and do another. It should not subsidize private publishing initiatives with government funds. It should not put its thumb on the scale for initiatives it likes, providing unfair advantages. It should not be the primary publisher for any online journal. It should stop dishing out PubMed indexing selectively, based on opaque judgment calls rather than transparent public criteria. NLM should manage NCBI and PMC more conscientiously, and make them stop competing with publishers and technology companies.

eLife should conduct itself in an above-board manner and stop using insider dealings to seek an advantage. Public officials should stop using public resources to affect private markets or provide advantages to businesses run by people they happen to personally agree with.

I have had the greatest respect for many of the people and procedures at the NLM over the years, but the problems I’ve described above are real, and they are solvable. Therefore, they should be solved quickly if the NLM is serious about providing an objective, reliable, and fair indexing infrastructure for online journals.

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Kent Anderson

Kent Anderson

Kent Anderson is the CEO of RedLink and RedLink Network, a past-President of SSP, and the founder of the Scholarly Kitchen. He has worked as Publisher at AAAS/Science, CEO/Publisher of JBJS, Inc., a publishing executive at the Massachusetts Medical Society, Publishing Director of the New England Journal of Medicine, and Director of Medical Journals at the American Academy of Pediatrics. Opinions on social media or blogs are his own.


63 Thoughts on "Something’s Rotten in Bethesda — The Troubling Tale of PubMed Central, PubMed, and eLife"

Powerful stuff! PMC’s behavior is outrageous. They are out of control. One wonders how much this has to do with the fact that both eLife and PMC are owned by major funders?

I’m a bit confused by the concept of PMC being “burned” by a publisher who “moved or stopped” their journal. Given that the papers exist, regardless of the publisher’s later actions, doesn’t it serve PMC’s archival mission to include those papers? What is the downside for PMC if they archive papers from a new journal and that journal then fails? Isn’t it even more important that PMC makes those sorts of papers publicly available? It’s not like the research in those papers stops being valid.

“Public officials should stop using public resources to affect private markets”: I couldn’t agree more. Let’s stop giving away publicly-funded research to commercial publishers who want to conceal it from the public.

A nonsensical and irrelevant comment on many levels. Thank you for that display of mental gymnastics.

PMC exhibits favoritism towards a journal with policies that are more closely aligned with the overall interests of the scientific enterprise. Traditional publishers scream cronyism while continuing to profit from raising barriers to the free exchange of scientific information. My heart bleeds, violins play, etc.

I do agree that PMC should make this favoritism explicit, though, and codify it in formal policy.

What policies are you referring to? The policy to allow funders to sponsor a journal using editors those same funders fund? Is that the policy that you believe is “more closely aligned with the overall interests of the scientific enterprise”? The policy that motivates a group to use insider influence to publish at taxpayers’ expense?

Can you explain why eLife is “more closely aligned with the overall interests of the scientific enterprise” than other fully OA journals published by other not-for-profits?

Kent, a powerful piece and something I have been fighting since Harold Varmus, Pat Brown, and David Lipman all decided to promote OA through E-Biomed, the predecessor to PubMed Central. For years, the procedures have been unevenly applied. When JMLA went onto PMC I questioned the appropriateness of the move but was willing to give it a pass since it was the Journal of the Medical Library Association. However, I was bothered by the fact that JBT abandoned its host platform for PMC when the editor was a member of the PMC Advisory Committee.

The American Physiological Society will soon be launching an OA journal in partnership with our sister society in the UK, The Physiological Society. Physiological Reports will launch in 2013 and I contacted Lipman to determine how to get listed in PubMed. He put me in touch with Ed Sequeira who provided me with the following information and comments:
“This is an interesting development. I didn’t realize you were moving in this direction. Good to hear about it.
There shouldn’t be any problem getting the journal into PMC. The process is similar to what you did to deposit NIH-funded articles from your traditional journals – the NIH portfolio arrangement.
Two bits of information that will help us:
• How many articles do you expect to have ready to publish the day you launch the journal officially?
• Who will be handling your production of XML and the deposit of files to PMC?
NLM wants to see a reasonable number of articles published before it approves a journal for PMC, but given the backing of APS and the Physiological Society, I expect the threshold to be low in this case.
We also need to evaluate a sample set of your files to make sure they meet PMC’s tech specs. If you’re using the same supplier as for your current PMC deposits, or someone else who’s accustomed to supplying content to PMC, this process should be relatively quick and smooth.
Before the journal is released in PMC, you’ll need to complete a PMC full participation agreement ( This is quite similar to the NIH portfolio agreement you have with us now, so I don’t see any obstacles there.
Lastly, your articles will get PubMed citations as soon as they’re live in PMC.”

So, even for established publishers, the rules appear to be flexible, but not as flexible as they are for e-Life. PMC and its leadership have to stop tilting the playing field to accommodate their friends and those whose publishing models meet their vision for the future.

Ed Sequeira and others at NLM have always been reasonable people. However, if this flexibility is provided for OA journals, that’s another thumb on the scale — what “direction” were you moving in that generated this flexibility? Seems like the OA direction.

It was in response to an inquiry related to a new OA journal we will be publishing in 2013 – Physiological Reports.

It seems the PMC has erred and broken the rules they established. Who knows their motives. Nevertheless, they should stop. The commercial and society/association publishers should file a formal complaint. I would think those who feel harmed could go to members of the National Academy of Sciences which has members on it who also are members of their editorial boards and/or editors.

I do not think single voices will be heard by indifferent bureaucrats.

Additionally, it appears that the Wellcome Trust has decided to become a player in the publishing arena. Maybe somebody will challenge their not for profit status, especially if they institute page charges and membership fees for publishing and accessing.

Those who state that scientists are being funded solely by governmental grants are living in the dark. Public funds may fund some of the research but seldom pays for all of it. Also, I would ask those who make such a claim to account for multiple authorship of an article in which only one of the contributors has a public grant.

The argument for OA is specious at best. It will and does cost to publish an OA article. But, now the grant money instead of going to research is going to some OA publisher and there is no indication that more readership will follow. Most interesting, there is no indication that the readership for the latest OA article on the intricacies of the homobox gene on mating behavior of the fruit fly has increased.

Interesting article but I’m a bit confused by your mention of JMLA. JMLA has been published in print form for quite a while, starting when it was called the Bulletin of the Medical Library Association (BMLA) in 1911. So it has more than met the 15 articles requirement you mentioned. In fact I still get the printed journal in my mail box four times a year. The printed issue mentions PMC as the Digital Archive of JMLA. You don’t mention whether the 15 issue requirement is in general (print or online). If it is just 15 articles (regardless of print or online) then JMLA already met that requirement, probably in 1912. Since JMLA still prints the journal and the printed issue states PMC to be the digital archive then wouldn’t PMC still be the secondary publisher?

I don’t know the details regarding eLife, but I don’t think JMLA makes a very good example in your argument. JMLA does have a website and it still does publish articles outside of PMC (albeit in print). Additionally while I received the October 2012 issue just this week, the October 2012 issue is not yet in PMC. So it isn’t offering current issue immediately upon publication either.

I agree there is a lot of confusion regarding “PubMed and MEDLINE, along with how PMC can be used as a backdoor into PubMed.” The problem is that eLife isn’t the only one exploiting it. Open Access publishers, for profit publishers, and association publishers, as well as authors are ALL exploiting the confusion. The requirement that works published from government funds has opened the door for non-indexed journals to squeek into PubMed via PMC. For example the journal Pharmaceuticals (Basel) is not yet indexed in Medline, it is forthcoming, yet if you do a search you in PubMed you will see approximately 20 articles listed. The reason is that the authors submitted them to PMC because the research used NIH money.

There is a blurring of lines between PMC, Medline and PubMed. PubMed houses PMC and Medline citations, and it is where researchers want their articles. Most researches equate PMC with PubMed and PubMed as being “in Medline.” Submitting their article to PMC not only fulfills the NIH requirement but it gets their article in PubMed (which they think of as Medline) and that is equally important because that is what “everybody” searches anyway.

I think the bigger issue is blurring of lines between PMC, Medline, and PubMed and the question why an article in a journal not indexed should be within PubMed, which in researchers’ perspective is in Medline. They see no distinction between PubMed and Medline. While I can’t speak to the quality of all the articles in PMC (and by default PubMed) from non-indexed journals, it does make you wonder about the quality. If the journal isn’t good enought to get into Medline then why is the article good enough to be found in PubMed.

I mentioned the other journals PMC puts on its platform to call attention to how they place themselves in the market both as a publishing entity and as a technology option.

I understand it was to call attention, but by your own words (15 issues and PMC as the primary publisher) JMLA does not fit in with your example. It has been published for more than 15 issues and has a primary publisher. PMC is the digital archive as evidenced by the fact that I have my October issue here on my desk but the October issue is not online in PMC. Additionally it has been indexed in MEDLINE since 2002. Your case is about a non established journal, not indexed in MEDLINE, squeaking into PMC therefore being accessible via PubMed.
I agree that is a problem but JMLA does not fit your case. The bigger issue is why are non indexed journals able to squeak into PubMed by using the PMC back door, thus giving them and their articles a certain perceived sense of MEDLINE credibility to doctors and researchers.

PMC is providing free hosting for JMLA, thus removing it from the market for hosting services. This isn’t the proper role of a government agency. CR&L is hosted by a commercial hosting firm. That is as it should be. As for whether PMC is providing timely, adequate online posting — you note the delay in posting the October issue — you get what you pay for. Right now, JMLA is published online by PMC.

“Free hosting”? Are you kidding? PMC is an archive. If PMC was a publisher, there’d be information about contacting the journal, author instructions, a reviewer log-in, etc. No, PMC only provides the text. That’s the entire point of its existence.

When PMC is hosting the only online version of a publication, and as someone defending JMLA before noted, if PMC hasn’t published it online, it’s not published online, well, that’s more than just being an online archive. That’s being a primary online publisher.

Kent, could you please stop referring to yourself as the “Publisher” of the Journal of Bone and Joint Surgery. I am fairly certain that you play no actual role in the physical conveyance of papers to your readers, and thus, while you may be overseeing the process of editing and review, you are not, by your own definition a publisher.

The definition of “publisher” at the organizational level is outlined in the post. The definition of “publisher” as a job is usually a bit different — usually a lead executive in charge of the business units necessary to execute the publishing functions. I refer to myself as “publisher” as a job title, not as an organization. I hope this helps you with the distinction.

Kent, I’m flabbergasted by this post. The purpose of PubMed Central (PMC) is to provide free full-text access to published research. If publishers choose to share their content with PMC, that’s a benefit for the public.
I could argue about many specifics, but the ROI for me would likely be very low. Suffice to say, I couldn’t disagree with you more. I’m very disappointed by this post.

Laura, if this is indeed the case, is there a good reason that PMC seems to favor some publishers over others (despite a similar willingness to share content)? That’s the point of this post–PMC has set up some rules for how they will operate to achieve the benefits you suggest, yet only some publishers are forced to follow those rules, and others are exempted. Is consistency and fairness too much to ask for?

Laura you seem to have missed the point entirely for you do not respond to it. What is going on here is what we call mission creep, where a federal agency takes off in new and inappropriate directions on its own. (By the way publishers do not choose to share their content with PMC they are forced to, but that is a different issue, stealing eyeballs and such.)

I’d be interested in the specifics you think are incorrect. Is it proper for a US government agency to provide free hosting and online publication for certain journals? Is it fine with you for those journals to be taken off the technology market because of this? Is it OK for eLife to get publishing services through PMC and backdoor PubMed indexing before they’ve met stated PMC policies?

Please express more than vague emotions. I’d be very interested in your specific intellectual disagreements with this post.

How many times do librarians need to tell you that PMC does not equal indexing? MEDLINE and PubMed are not equivalent: .
Indexing a journal in MEDLINE – assigning subject heading to each article – involves a tremendous amount of work by the highly educated, trained NLM indexers. Before PubMed, the public had limited access to the work of MEDLINE. PubMed exists for the public. We’re lucky to have it.

Here’s an example of the PMC/PubMed interaction: PLoS Currents is not indexed for MEDLINE. The article data is sent from the publisher to PMC, which then forwards citation data to PubMed without assigned subject headings. As you’ve discovered, the same is true for quite a number of journals that have been added only to PMC. Only the basic citation data is in PubMed, no added value from human indexing. I don’t understand why you think this is a bad thing.

Adding a journal to PMC does not entail the rigorous process of adding a journal to MEDLINE. For MEDLINE inclusion, a committee of experienced researchers (MDs and PhDs) meets 3 times a year to make recommendations on about 140 journals. The selection process is not taken lightly by these experts. Accepting a new journal for indexing in MEDLINE also means even more work for the indexers.

A journal that meets basic scientific standards and very specific technical requirements will have a much easier time getting added to PMC than MEDLINE. NLM has a serials collection of over 20,000 titles, but only about 5,300 are indexed in MEDLINE. You might notice that the technical requirements detailed at are much more extensive than the scientific requirements.

Each journal has to decide whether it’s worth having content available for free at PMC. Worried about losing site traffic? About not selling as many ads? That paid subscriptions will decline? Well, maybe it’s not worth it. Some prominent journals only provide selected “open access” articles to PMC. Others provide articles after a 6-month delay.

If you have an argument with the entire premise of PMC, write a post about that instead.

The point isn’t what librarians know and what some publishers know. It’s what editors, authors, researchers, and practitioners think. And most of them think PubMed and MEDLINE are equivalent. Being in PMC does equal indexing in PubMed, which is viewed by many in science as equivalent to MEDLINE indexing, which is why its such a sneaky way to leverage PMC/PubMed.

Part of this post was an argument against the premise of PMC — competition with journals and competition with publishing technology companies, partly by leveraging PubMed indexing to provide an advantage.

I appreciate the lecture about the distinction, but the point is that the distinction is not well-understood outside some very tight circles, and even the backdoor into PubMed that PMC offers is not well-understood — nor is it opened for all. In this case, eLife seems to have had the secret password.

My point about JMLA’s October 2012 issue was to illustrate the PMC is not acting as the primary publisher it is acting as the ARCHIVE. I am a subscriber and I do get what I pay for because I have the current issue (October 2012) from the primary publisher in my hands now. There is no requirement for journals to be online to be in PMC. Your continual insistance to lump JMLA with eLife which hasnt met any of the requirements is short sighted and stubborn. Bottom line JMLA has met all established rules eLife didn’t. You dilute your argument by adding a journal that technically qualifies to be in PMC.

We’re talking past each other. If JMLA had another online presence, another online instance, then it wouldn’t be involved in this discussion. But its primary online version is the PMC version. This has two effects — it makes PMC the primary online publisher of JMLA (a fact that widens the readership of JMLA beyond its print subscribership), and it makes PMC competitive with publishing technology companies. If JMLA were hosted on a commercial publishing platform at the same time, ala CR&L, then this would be JMLA’s archive. Because JMLA is not, PMC is for all intents and purposes JMLA’s primary online version, which makes PMC JMLA’s primary online publisher. We’ve had to wait to post research out of JMLA on this blog before because the online version at PMC was not available. This means there’s nothing else out there, and PMC is the primary version. And, like I wrote in the post and above, because the PMC version is the primary version, it means PMC is the primary online publisher and PMC has removed JMLA from the online hosting marketplace.

I do get insistent and stubborn when people try to elide the facts.

I think there are two separate points that are being conflated here:

1) PMC has broken their own rules, and shown favoritism to a particular publisher, which has nothing to do with JMLA.

2) PMC is acting as the de facto publisher for some journals, which includes the JMLA.

This is utterly astonishing, thanks Kent for picking this up and bringing it to our attention.

Not only does eLife already enjoy the enormous advantage of being bankrolled by super-rich funders (allowing it to behave in a massively anti-competitive way by waving APCs), now it gets the added bonus of “under the counter” entry into PubMed without all those inconvenient years of waiting to pass the quality control test! It’s not even like it’s a journal from a publisher with a proven track record!!

Truly disgraceful!

“Not only does eLife already enjoy the enormous advantage of being bankrolled by super-rich funders (allowing it to behave in a massively anti-competitive way by waving APCs), now it gets the added bonus of “under the counter” entry into PubMed without all those inconvenient years of waiting to pass the quality control test! It’s not even like it’s a journal from a publisher with a proven track record!!”

I don’t believe that is true.

Articles that are in PMC I believe are all searchable though PubMed via “free-text” searches but they are not indexed with MESH headings and are not necessarily in PubMed/Medline. The comments on this blog keep talking about this as though it is some big collusion but I believe it is true for all articles in PMC and does not necessarily mean they are in PubMed/Medline.

I was told this by the staff at NLM when my journal was accepted into PubMed and then archived in PMC. We put two years worth of articles in to PMC when it was accepted but they only indexed the the latest year in PubMed. The previous year was searchable in PubMed (I know this for a fact) but not by MESH headings and they indicated that was true for all of PMC.

Kent Anderson has posted two very strident (my opinion) posts about eLife concerning COIs and collusion. Kent has every right to his opinions but he has his own pretty large COI as a CEO/Publisher of a journal competing directly with eLife. I hope the readers of the Scholarly Kitchen consider this when reading the blog.

To the reader and author, there is absolutely no difference between being indexed in MedLine and being listed in PubMed search results. These are nuances, which are not well understood by the research community. Is the journal in PubMed? If the papers show up in the results of a PubMed search, then for most, if not all, the answer is yes.

Kent does have a horse in the race here, as do most commenting (and reading). It’s not a conflict of interest to ask for a level playing field for all publishers.

Honestly, I don’t consider our journal to be in competition with eLife — not even indirectly. The thought never occurred to me, until you offered it as a bit of a jab. ELife is entering as a new competitor, but it’s not at all clear who or what it’s competing with.

Plus, I always welcome competition. Done right, it makes everyone better. But when competition is based on structural conflicts of interest (as it is with eLife, wherein funders are funding a publisher and the editors running that publication) and on cronyism with a US government agency responsible for bibliographic functions, that’s not the kind of competition any of us can condone.

Perhaps I phrased that poorly I think subscription publishers do have a COI with evaluating other journal funding models such as eLife. These models are at least in my view in competition not with your journal per se but with the whole subscription funding model.

Really? That’s even harder to get my head around. There is little to no evidence that OA journals compete with subscription journals. As I’ve noted in other posts, submissions are going up everywhere. Again, legitimate competition is fine. But to use cronyism, to misuse government resources, and to compete illegitimately? I can’t abide that. Can you?

Kent – I’m confused by some of the conflation of issues in this post.

There is a long argument about PMC as a backdoor into PubMed vs. the waiting time for Medline. This is a function of the role of PubMed as a superset of citation data including content in PMC and several other sources as well as Medline, so it seems that your argument should be about the relationship of PMC to PubMed, or more specifically the inclusion criteria for PubMed, not about eLife. If Medline is thought of as a value-added service applied to more highly curated content (I don’t know if medical library colleagues would agree with that characterization but it’s one way to think of it), some of the apparent conflicts and claims of unauthorized ingress go away in my view. But you may have an argument that there should be a more lightweight process for inclusion of non-OA citation data in PubMed with a similar vetting process as that used for PMC.

With respect to eLife, one thing I didn’t see in your post (but perhaps I missed it) was whether eLife leapfrogged over other journals waiting in line for inclusion in PMC (not Medline). If not, then the fact that the NLM selection committee may have been flexible in its treatment of eLife, a journal surely bound to meet its scientific criteria, doesn’t seem like a criminal infraction. Ed Sequeira’s note to Marty Frank seems equally accommodating: “NLM wants to see a reasonable number of articles published before it approves a journal for PMC, but given the backing of APS and the Physiological Society, I expect the threshold to be low in this case.” So i’m not sure where I see the cronyism and unequal treatment, unless it’s been shown that there were other journals waiting in a PMC queue that met all of the criteria (including technical criteria that might affect ingest readiness) that were pushed to the back of the line. Since PMC is a full-text repository, it’s hardly surprising that it’s responsive to requests for full-text deposit from qualified journals.

I think the primary publisher argument is weak with respect to eLife, unless they decide to abandon their plans to go live on HighWire. Here again, it’s hardly a scandal that PMC, as a fulltext repository chartered to support wide public dissemination of the biomedical research literature, would be willing to accept deposits of qualifying content a few months in advance of eLife’s go-live date. That hardly makes it a primary publisher. But your post does rightly highlight changing notions of dissemination and the role of repositories in an increasingly online and increasingly OA world. Is arXiv a primary publisher? Should it be? Would an embrace of this role of repositories by publishers help to lower the costs of formal publication and contribute to sustainability and affordability? I’m not making any assertions here so much as articulating what I see as a set of questions that we’re all grappling with.


I’ll respond point-by-point in both places you’ve put this comment.

The argument about PMC being a backdoor into PubMed is that, to most people outside a small circle, MEDLINE and PubMed are synonymous. Publishers, authors, readers, and I’ll bet a number of librarians either think so, or haven’t stopped to think there might be a difference. Inclusion in PubMed is a carrot offered by NCBI for joining PubMed Central, so they have asserted value and, I believe, done nothing to clarify the situation because the confusion serves them well. Why should a business model choice give you such an advantage? That’s another implicit question. But there has been confusion and not clarity about what PubMed is, and that confusion has, I believe, been exploited to drive PubMed Central forward. In the case of eLife, this was especially egregious because they got into PubMed without meeting normal NLM requirements for even PubMed Central inclusion.

Which brings me to your second question about leapfrogging. Yes, eLife leapfrogged other publishers waiting for inclusion in PubMed Central. If you read the original post, you’ll see that another publisher I was speaking with was receiving emails from PubMed Central about their inclusion criteria, which required 15 articles and data submission, review, and approval. This journal had been requesting inclusion for months, and this email was just confirming the requirements, which PubMed Central confirmed in the manner shown. In the meantime, eLife, without having published anything elsewhere (a PMC requirement), was ushered right into PubMed Central, and indexed into PubMed. You say “it’s hardly surprising that [PMC]’s responsive to requests for full-text deposit from qualified journals.” That’s the problem — eLife wasn’t, by PMC’s own rules, “qualified.” It cut the line with PMC’s tacit assistance, and nobody at NLM can give me any specifics about who approved this, when it was requested, and when it was approved. That sure sounds like cronyism as I defined it in the original post, don’t you think?

There is a related issue here, which is conflict of interest (COI). COI is often based on appearances — apparent COI is COI. A scrupulous organization wishing to avoid the appearance of conflicts of interest will do whatever it can to be attuned to these and not make decisions that appear as if they are serving interests other than their mission and purpose. In this case, PubMed Central allowed two consecutive terms of Wellcome Trust board members, the latest being their solicitor. Then, when Wellcome launched a journal with two other funders, did PubMed Central behave scrupulously and draw a bright line between itself and the interests of its board members? No, they did exactly the opposite. They invited Mark Patterson in to speak via videoconference in an unprecedented manner, then without leaving an apparent trail, moved to rush eLife content onto their platform and become its primary publisher. That’s the kind of scandal-level COI stuff of legend, the kind that gets leaders of organizations into serious hot water. And David Lipman has said he feels no need to respond. How’s that for admirable leadership?

The “primary publisher” argument is really important, and I think it’s important to think hard about this, because each step is important. First, what is a US government agency doing helping a private enterprise launch itself? That’s not its role, and not what taxpayer money should be used for (funny how OA uses taxpayer funds when its suits its purposes, even if there are three billion-dollar charities backing the new business). Nobody else is publishing eLife — not eLife, not HighWire Press, nobody. PMC is the only place you can get the primary version of the articles. PMC is also the primary publisher of JMLA and at least one other journal. That’s not right. arXiv is not a primary publisher because it’s defined itself as a repository, but you could argue the case. In any event, eLife has defined itself as a journal, and PMC is acting as an extension of eLife and providing the primary and sole version of eLife content to the world. It’s not its secondary, archival, repository publisher. It’s its primary publisher. Imagine if I went to a library, and the librarians agreed to take my unpublished work and print, bind, brand, and disseminate it for me under my brand and theirs. That library would become my primary publisher, especially if it was the exclusive source of my works. It might be a library for everyone else, but it would be a publisher for me. That’s roughly what PMC has done on behalf of eLife. And, yes, actually, eLife could sever its contract with HighWire given what PMC has provided them with. At least two other journals have been taken off the market because PMC serves as their primary publisher. Should PMC even be creating this possibility for eLife, and this reality for the other two journals? I think it’s way, way, way over the line here.

This whole situation is wrong — from a conflict of interest perspective, from a government role perspective, from a cronyism perspective, from a commercial perspective, and from an accountability perspective.

Kent, I agree with you summary with one exception, namely the appearence of COI is not COI. It may be evidence of COI or just an appearence. Whether this appearence matters or not depends on the situation. I mention this because accusations of COI based solely on alleged appearances are common in policy debates and they are often bogus. It is a standard political tactic.

It is clear that PMC has done something wrong with eLife, for the reasons you give. But whether the Wellcome advisory members had anything to do with it is simply not known. The possible connection is worth pointing out but that is as far as it goes without further evidence. Agencies cannot refrain from dealing with the organizations whose people advise it. If they did there could be no useful advisory groups.

The reason why the appearance of conflict of interest is a starting point is because that’s what an organization has to manage once the potential for acting on that conflict exists. The definition of a conflict of interest underscores this: “A conflict of interest is a set of circumstances that creates a risk that professional judgment or actions regarding a primary interest will be unduly influenced by a secondary interest.” There is no need for further evidence to assert a conflict of interest. It is based on risk, circumstances, and appearances.

The actual act of impropriety is the act of impropriety — e.g., insider trading. The circumstances and arrangements that created the potential for that is the conflict of interest or competing interests.

What PMC needed to do with the risk of COI regarding Wellcome (and potentially others, like PLoS) was to ensure that any actions or decisions subsequently actually showed that they realized these conflicts existed, and that they acted to reduce the risk to themselves, the members of their NAC, or their reputation. That’s how you correctly manage a conflict of interest — through recusal or refusal.

So, there were competing interests (aka, conflicts) on the PMC board. How did they manage them? Well? Poorly?

In the case of eLife, they not only invited the managing editor for eLife in for an unprecedented meeting via videoconference, putting their Wellcome board member’s conflict front and center, but then short-circuited their own processes to get eLife up and running before it had met their published criteria for inclusion. This was extremely unwise for an organization with conflicts of interest on its board, and indicates to me an arrogance or ignorance regarding conflicts of interest and how to manage them. Again, recusal and refusal. They should have been responsible enough to know that it would be viewed as improper for a new entity supported by one of its board members to be given special treatment. The conflict of interest was incipient. They failed to manage it responsibly. There is no indication that the Wellcome board member recused himself from any deliberations regarding eLife, and PMC didn’t refuse to help them despite its board containing conflicted members.

Conflicts of interest can be handled easily, usually through disclosure, when they are structural and just based on appearances. People can judge for themselves if the conflicts affected behavior or decision-making. In the case of PMC and eLife, the conflicts existed, and were very poorly managed by PMC, leading to actions that really smack of insider dealing.

Just a small point: to say that eLife articles are available ONLY on PMC is inaccurate. Quoting from, “eLife content is also available on Github, scribd, and Mendeley.”

The Mendeley items only contain citation data, but github and scribd both contain PDFs of the articles.

PMC is clearly the most popular access point for eLife content, but it’s not the only one.

Yes, there are downstream copies being placed on commercial platforms, but eLife points to NCBI as their primary publisher.

Most importantly, PMC is the only one of these that also went out of its way for eLife. The others probably don’t even know or care that eLife has posted PDFs on their platforms. PMC definitely participated in turning itself into eLife‘s primary publisher.

I also think they made these deposits on other platforms after this post came out, and possibly in reaction to it.

The Scribd and GitHub PDFs were posted on October 16, one day after the first batch of articles was published.

Did you just call a 501(c)3 (the designation for a genuine, no-foolin’, tax-deductible charity) a “business” in “private markets”? I can think of contortions of language that could equate those two, but it would require contortions of language.

A 501(c)3 is an organization that cannot distribute its earning to the benefit of private interests or lobby for political purposes (hence, it is run not for profit). Every 501(c)3 is a business, just a business with a very particular purpose, from which it cannot stray (or it runs into having unrelated revenues, which can be taxed differently or, if they are too far unrelated, too large, and too consistent, could lead to the business losing its 501(c)3 status). They are commonly called “charitable organizations” but they they just work under different rules in the tax code, and have different restrictions, mostly based on their missions. Every 501(c)3 is subject to the realities of business — make enough money to sustain itself, follow IRS and employment law, follow good accounting practices, watch its expenses, and compete in the marketplace, whatever marketplace that is. It’s this competition in the marketplace that puts 501(c)3’s into the “private markets” in many cases. For not-for-profit publishers operating as 501(c)3s or societies with strong publishing arms (which often make a lot of the revenues these 501(c)3s rely on to defray member fees and pay for educational activities), they have to compete with Elsevier, Wolters-Kluwer, and Springer, among others. They also have to compete with one another in some situations. For the government to give an advantage to one organization over all others by helping them cut the line at PMC, launch early, avoid paying technology costs, and so forth, they are affecting organizations competing in private markets, and 501(c)3 are legitimate business organizations in those markets.

I guess you think explanations are “contortions of language.” Your choice. I guess you have a hard time with details and logic, and believe those equate to contortions. What you may not realize is that every 501(c)3 has to start as a corporation, then apply for tax-exempt status, which may or may not be granted. Therefore, each one starts as a business, and has to register as such before granted any tax-exempt status.

But you go ahead and enjoy splitting hairs, as if it matters. The facts are the facts, even if you seek to dismiss them as “contortions.” I think you’re the one doing the contorting/distorting.

At OUP, we prefer the term “profit-for-purpose”, but we are technically a not-for-profit. But we sure as hell run things as a business, and if we don’t turn a profit, we have no ability to grow, to invest and develop new technologies or experiment with new types of publishing, no ability to weather any financial downturns or disruptions in the market. A not-for-profit that doesn’t make a profit will not exist for very long. That’s why eLife is putting such effort into developing a sustainable business model.

Even if one accepts your concept of what a not-for-profit is, then why should the US government favor one (eLife) over every other 501(c)3 not-for-profit scholarly publisher?

As the old society saying goes: We are not-for-profit but not profitless…

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