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Journals wishing to be included in PubMed Central (PMC) have to apply — unless they hold a membership in the old guard of open access (OA) publishers. In the case of eLife, that membership was granted via the long-standing cozy relationship between PMC and Wellcome Trust. In the case of F1000 Research, it seems the membership came from a shared history with BioMed Central (BMC).

The final 200+ pages of items responsive to an expanded “F1000 Research” portion of my Freedom of Information Act (FOIA) request show not only that PMC leadership once again violated its stated policies by inviting F1000 Research into PMC, even assigning a long-term contractor to reach out, but also shows another poor handling of conflicts of interest.

BMC was founded by Vitek Tracz in 2000, and sold to Springer Science + Business Media in 2008 (Springer itself was recently acquired by a private equity firm). In 2006, a journal, Biology Direct — edited then, as now, by Eugene Koonin, NCBI, NLM, NIH; Laura Landweber, Princeton University; and David Lipman, NCBI, NLM, NIH — was launched at BMC, when Tracz was still in control. Tracz subsequently launched F1000, which in 2012 launched F1000 Research. These facts provide some context for what follows.

F1000 Research Avoids Falling through the Cracks with PMC’s Help — Journals wishing to be included in PMC have to start the process themselves. As stated in PMC’s instructions, “Publisher initiates the application process,” which involves sending an email with specific information to PMC in order to start the process of evaluation. There is no evidence these emails existed in the case of eLife, and apparently PMC catalyzed the process in the case of F1000 Research.

On September 20, 2012, David Lipman sent an email to one of the main contractors for PMC, Chris Kelly:


Vitek cc’d me on the message about them applying for PMC inclusion. Let me know if you have any questions. I had some real concerns initially about what they were doing but overall, I’m very satisfied right now.


The email Lipman cites here is one that I do not see in the files, and since this particular FOIA request is complete, I can only speculate that it didn’t contain any of the terms I queried on — “F1000 Research,” “F1000,” or “F1000R.” It may have been a more general email about a new journal.

On the morning of October 2, 2012, Lipman emails Kelly again (there is no evidence that Kelly responded to Lipman’s first email):


Did f1000 submission come in yet?


About 40 minutes later, Kelly replies:


We haven’t been contacted by F1000 Research about starting up the process yet. Would you like me to contact them to get the ball rolling?


Thirty minutes later, Lipman responds:

Yes – I think something fell through the cracks.

Just under 30 minutes after that (at 11:38 a.m.), Kelly confirms:

OK, David. I’ll follow up today to get things moving.


F1000 Research applied the next day.

A benign reading of this could make Lipman look like a helpful public servant with good connections. However, given past behavior, including his efforts to provide eLife with launch assistance while concealing this from the PMC National Advisory Committee along with his eagerness to get PeerJ included in PMC because “it could be a very important journal for us,” and this only adds to an emerging track record as mogul or king-maker. Add to this an apparent absence of such activism for the dozens or hundreds of other open access (OA) journals, and the silence of omission speaks loudly as well.

Flexibility has been noted around PMC processes in the past, and a certain amount of this is understandable. But there seems to be a bright line between being accommodating and being activist. Lipman crossed into the activist role yet again in the exchange above, by assigning staff to prod a publisher — and one Lipman has a history with — to apply. He could have merely emailed Tracz himself to say nothing had yet arrived, and left it at that. Instead, he assigned a PMC contractor to reach out.

The Insiders’ Game — This event also adds to the perception that OA currently has a core group of insiders running the main stage. I talked about this in a post recently about the leadership changes at PLoS, which involved swapping among eLife and PLoS leadership teams. Certainly, the founder of BioMed Central and current owner of F1000 receiving special treatment doesn’t help this perception, especially when Lipman has been and continues to be the editor of a BMC journal, Biology Direct.

Conflicts of Interest at NCBI and PMC — On February 7, 2013, Vitek Tracz emailed Eugene Koonin, a senior investigator at NCBI and a co-editor, along with Lipman, of Biology Direct on BMC, requesting that Koonin, who is also a faculty member in bioinformatics for F1000, send an email to his colleagues promoting F1000 Research. Tracz drafted an email Koonin could use, and notes in his message that F1000 Research is now facing a “battle for papers.”

On February 11, 2013, Koonin replies, copying Lipman on his reply:

Dear Vitek,

Thank you for your interesting update on F1000Research. This new journal certainly is a worthy undertaking, and I especially appreciate the post-publication open review system.

I think this is one of the more attractive peer review options available, and accordingly, I think the journal is almost “doomed” for success. This said, I am afraid that I am not entirely comfortable to promote the journal actively. The reason is that the entire publication model of F1000Research clearly resembles the model implemented in Biology Direct, an Open Review BMC journal that I have been co-editing with David Lipman and Laura Landweber over the last few years, with considerable investment of time, thought and effort. I am strongly committed to Biology Direct and therefore would rather not express vocal support for other journals with similar approaches to publication.

While for the above reasons, I will not actively engage in promoting F1000Research, I wish your journal every success, and I am practically confident that such success is coming.

With best regards,


That evening, Lipman replies to Koonin:


I know Vitek respects you highly and I’m sure he appreciated you taking the time to respond to his message. Thanks for sending this along.


This gets us into an interesting thicket of competing interests, with Lipman and Koonin having many all at once but responding very differently.

Koonin recognizes his conflict and excuses himself from helping the new entrant. He does not resolve his conflict of interest (i.e., does not step down from F1000 or Biology Direct), but he recognizes its existence and responds as someone with a conflict might — that is, choosing one interest over another (in this case, choosing Biology Direct over F1000).

Lipman apparently does not recognize the conflict of interest between running PMC and working on the indexing of a competitor for Biology Direct, a journal he co-edits for a competing company. If he were to acknowledge this conflict, his best course would be to recuse himself from any involvement. As shown above, he did not recuse himself or even informally sideline himself, and instead became actively involved on behalf of his friend and former boss at BMC, directing contractors to ensure the journal was moved forward as expeditiously as possible.

Even faced with an email from a co-editor from the same journal citing a conflict of interest, Lipman does not acknowledge or respond to the problem. This all is reminiscent of Lipman’s apparent inability to recognize and avoid or resolve conflicts of interest around eLife and Wellcome Trust.

Consternation at PMC over F1000 Research I’ve said before that “F1000 Research just makes my head hurt.” It seems I am not alone. Judging from glimpsed gained through emails internal to PMC, I’m not alone.

On January 23, 2013, Rebecca Stranger wrote to Joyce Backus (Director, Division of Library Operations) and Jerry Sheehan (Assistant Director for Policy Development), copying David Gillikin:

Wow, F1000 is very confusing. I hope this brief synopsis helps. Rebecca

David, thank you for your input.

There are other signs of frustration with both understanding and implementing the F1000 Research model in the emails — brief comments and asides not worth reproducing here. There are also emails expressing dismay about how F1000 Research presented inclusion in PMC initially. On January 25, 2013, Chris Kelly wrote to David Lipman, copying Ed Sequira (Kelly’s one typo has been preserved):


I wanted to make sure you saw this – it was posted by F1000 on Jan. 14 but I just saw it today. We’re not close — have not received sample files yet — but they’re telling authors citationsn will start appearing in PubMed “in the next few weeks”. That was two weeks ago.

But my biggest concern is the misleading statements about the timing of citation submissions to PubMed in the final paragraph. PMC sends a citation to PubMed after the article is fully processed through our system, QA’d, and released — no guarantee this will be the same day it is deposited — and then  it takes 2-3 business days after that for the citation to actually appear in PubMed. What they’re saying here is wrong.


“We are very pleased to say that F1000Research has been approved for indexing in PubMed.  Don’t rush off to go and look for our articles there yet though, as there will be a short delay before the first ones appear – it should happen in the next few weeks.

We have agreed with the NLM Selection Committee that only articles that pass our peer review process will be listed in PubMed, and of course also deposited in PubMed Central.  This is a similar arrangement to that agreed with Elsevier last year with regard to indexing in Scopus and Embase; again, our articles will start to appear on these sites very shortly.

With our record for publication time of 30 hours and our record for receipt of referee reports of 24 hours, you could find your article listed in PubMed in under 3 days from submission!  Could prove rather handy if you need something quick for those looming grant deadlines or you need to ensure you don’t get scooped.”


Rebecca Stranger is who first flagged F1000 Research’s blog post, quoted above. She forwarded it to Kelly a few hours before the email above was sent. In an email to Sequeira and Peter Cooper, Kelly characterized the F1000 Research post as “pretty misleading stuff.”

Conclusion — At some level, this is just more of the same — more coziness within the old guard OA community and more unmanaged conflicts of interest, with some new signs of friction between F1000 Research and PMC over promotional statements.

We’re able to see this behavior because it involves a US government agency, making everything part of the public record. After all, they are supposed to be serving the needs of the taxpayer and the research community, including OA publishers who might fall outside their inner circle. These recently acquired documents add to the impression that publishers need to be part of the new “old boys” network to qualify for special treatment. There are signs elsewhere of this old boys network, with one stark example being PLoS’ move to hire a former PLoS and PMC and eLife luminary as its new CEO. Such internecine networks also foster a feeling of insulation and inherent infallibility, which can help create blindness to conflicts of interest — after all, it’s “just us,” and if we set the standards for our own behavior, who can possibly criticize us?

OA publishing may have wanted to dismantle barriers and free up the publishing landscape. Instead, it seems to be as prone to cronyism and favoritism and blind spots as any other human endeavor, which is why we need to — just as we do with every form of publishing — keep an eye on it and its special weaknesses and vulnerabilities.

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.


17 Thoughts on "PubMed Central and F1000 Research — More Signs of Favoritism and Activism, and More Conflicts of Interest"

There is definitely a faction for whom what’s being done is less important than who’s doing it, which I find terribly disappointing. For example, when CHORUS was first announced, much of the reaction was a defensive “this is a land grab”, rather than, “wow, publishers are finally seeing the light and trying to help,” or at least, “hurray, more articles will be freely available.” When Cold Spring Harbor Laboratory, a not-for-profit cancer and neuroscience research institute announced BioarXiv, a new attempt at a biology pre-print server, they were again accused of a “land grab” and derided for not having the right “OA credibility”.

The research literature should not be controlled by an exclusive club. One of the strengths of our current system is that anyone can start a BMC or a PLOS or a Hindawi, and the effort is judged on performance and results, rather than who’s behind it. It’s important to maintain this openness and offer a level playing field for all to experiment, lest the system become stagnant.


What you have relayed is a story of cronyism. The question is what can be done about it?

The OA publishers who aren’t getting equal treatment should write to the head of the NLM and NIH. The PMC NAC should address the issues at their meeting this week.

If those don’t work, the OIG might need to get involved.

As an enthusiast for open access, a former board member of PLoS, and a friend of Vitek, I think that it’s wonderful that F1000 Research has been rapidly entered into PubMed Central. I told the STM meeting in Frankfurt in the mid-90s that universal open access had to come. The publishers thought me mad–and many probably still do. Slowly and surely my prediction is coming true, but it’s a long, slow process—held back in large part because of the vested interests so ably represented in Scholarly Kitchen. The process is too slow, and I applaud anything that can be done to speed it up. Admitting eLife and F1000 Research rapidly to PubMed Central are steps that will help.

Anybody who is getting tired of the hot air in the Scholarly Kitchen and would like a fresh view might care to read my blog on why F1000 Research is so important.


The problem isn’t so much that either journal was admitted, nor that either journal was admitted rapidly. These are both good things.

The problem is that both received special treatment not available to other open access journals. It’s particularly disturbing that a privately held, for-profit company gets a speedy entry and extra help while not-for-profit efforts owned and run by the academic community have to wait in a slow line because they’re not part of the in crowd.

I think we would both agree that PMC admittance would benefit from being as rapid as possible, from declaring a clear set of rules and adhering to those rules, from treating all journals in a fair and equal manner and being as transparent as possible.

It is unsurprising that a self-proclaimed member of the OA old guard would see no problem with his old friends giving and receiving special treatment. More of the same redux

Do you fret, Kent, about making money from barring access to science, when access can do great good, 99% of the value of the research is in the research not the publication processes, and most of the research is funded with public money? It seems to me like an ethically dubious occupation.

Much to unpack here.

First, publishers do not bar access to science–the paper written about the research is not the research itself. Barring of what you refer to as 99% of the value of research comes from patents, and is done not by publishers but by researchers and their institutions. So the phrase “making money from barring access to science” would fairly describe any researcher who holds a patent, any university with a technology transfer office, any technology company, and really, any hospital. Do you consider these ethically dubious institutions that should be fretting?

Second, Kent, like many of us, works for a not-for-profit, in his case publishing the journal for a research society. Unlike F1000Research, any surplus generated is returned to the research community, rather than going into the bank accounts of businessmen and investors. Is keeping funding within the community to be used for the benefit of the community something to fret about?

Also of note, Faculty of 1000 itself is a subscription service, barring access to science as any subscription product does. I assume you’ve voiced your objections to this to your close friend.

Easy words to toss around, harder to make them mean anything. Do OA publishers make money by barring access? Yes, by barring access to a citable object — they bar scientists from publishing, not readers from reading. Both publishing and reading barriers are relieved with a dose of money. There is nothing unethical in asking people to pay money for something they want. In the case of OA, they ask authors to pay for a citable object, which authors want. In the case of subscription publishers, they ask readers to pay for something they want, which is an article they think is relevant and interesting.

I think your ethical dilemma is a straw man.

But you are making money from restricting access, and you are making money on value added by others. It’s a model that had to be “found out” and will inevitably end.

You state

“Reviewers are encouraged to read papers quickly and to approve if the paper seems acceptable in that the conclusions are supported by the methods and data. (It seems to me that this can almost always be the case if the conclusions are suitably cautious.)”

This implies cautious conclusions will be more likely to see you published. Leading perhaps to cautious experiments. And so to cautious science.

Is that really the incentives you want open access to promote?

And I’m staggered by your decalration of interests. $1000 to review a book for a journal! Think about that again: $1000 for *post-publication review*! Is that a utopian view of the future?

Thank you for your comment, but you’ve misunderstood. The current laborious and bureaucratic peer review system, which by definition tends to be wary of truly original science, is the biggest barrier to bold science. The light system of F1000 Research will encourage the publication of such research, but it will also make easier the publication of less exciting research–so long as the authors are cautious in their conclusions. One of the biggest problems in scientific publication is exaggerated claims based on limited data.

Your critique of the current system may well be right in some, but not all, cases. But maybe that’s at the grant level? Ground-breaking research – when funded – gets published.

Will grant applications be post peer reviewed?

Plenty of less exciting stuff is also funded and published currently of course.

So I’m confused as to what problem F1000 really solves. Is it going to reveal epoch-making stuff that is currently censored (by your latest argument) or unleashing more routine stuff for us to wade through (by your original blog comments).

This is an interesting topic. I think the favoritism seen here is similar to what happens behind closed doors every day when papers are reviewed in the current system (pre-publication peer review). Probably the same case in grant review as well. The good ol’ boys network to be short-defended by the good ol’ boys.

I am interested in the topic as I am working to develop an open access journal (TheWinnower.com) that will solely employ post-publication peer review and will publish papers for $100. However, I am “just a graduate student” without connections like F1000 or eLife. Without these connections I dare not even approach Pubmed for listing.

I find it a bit ironic that journals which promote transparency and open review for scientists often seem to operate without it.

I’d be careful casting aspersions on current peer review practices. There are problems but generally they work well unless someone intentionally lies in their work. The PMC old boys network took a lot of work to reveal and describe. I’d suggest you find evidence before drawing conclusions.

The real peer review takes place after publication. Much like your comment came after my comment was posted. Current practices (pre-publication) have major problems that are not limited to researchers lying.

See the following for evidence:
Nicholson & Ioannidis, Nature 2012
Nicholsom, BioEssays 2012
Horrobin, JAMA 1990
Rothwell & Martyn, Brain 2000

This is an excellent expose and thank you for your hard work and dedication to bring it to the community’s attention.

I’ve had a recent similar experience with PMC and Medline, and for fear of being “slammed” on our next review, I prefer to post anonymously.

While I can be dismissed as a “disgruntled publisher” there were numerous objective errors and obvious signs of a careless review. For example, our editorial board is replete with physicians, researchers, academicians, specialists and clinicians who are “household” names with enviable academic and clinical careers and sterling reputations – the very people who are principal investigators, conference, journal and society leaders, and seminal textbook authors who are published in Medline with hundreds of citable objects…

The Medline reviewer scored it 1 out of 5 for quality.

Essentially I believe they came to the conclusion first, then simply scored it low enough to justify their conclusion to keep us out of the Index Medicus and PubMed. I presume they based it upon being a “nobody” publisher and a nontraditional opinion format. We may not be a traditional “research” journal, there are many instances of powerful publishers getting into the Index Medicus with similar “nontraditional opinion” type journals (Blackwell, Elsevier, Springer).

This decision has an impact on revenue models. As a consequence of being left out of the Index, our material will not meet 21 USC § 99.3(j)(4) definition of “Medical Journal” which requires:

“4) That is indexed in the Index Medicus of the National Library of Medicine of the National Institutes of Health;”

This definition is carried into the “Good Reprint Practices” guidance of the FDA (http://www.fda.gov/RegulatoryInformation/Guidances/ucm125126.htm) from which pharma companies use to determine the proper parameters for safe reprint buying. Because of Medline’s decision reprint revenue is unavailable to support the publication and consequently we are changing its revenue model from Free Access to Subscription.

Sarah Calhoun (listed as a Contractor for PMC) communicated our rejection as :

The primary reason is that the journal does not contain traditional research or review articles;
therefore, it is not appropriate for inclusion in PMC.

Considering PMC does not publish any inclusion review criteria, I guess this is their prerogative.

While I agree we are not a “traditional” review journal, I would have appreciated some of the F1000 “special attention” to debate with PMC that in fact there are dozens of similar formatted articles included in PMC and MEDLINE already and that stating we are not traditional is hypocritical to content already in PMC and MEDLINE.

I’ll keep an eye out for OIG action to address the cronyism – and the revenue that is bestowed upon indexed publications.

Thanks for your tireless work in this regard – its a serious problem and I appreciate your dedication to pulling back the curtain (particularly on a journal that isn’t even “final” when indexed and can be modified as the post-publication peer review comes in).

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