Preprint repositories gaining traction

A preprint “is a version of a scholarly or scientific paper that precedes publication in a peer-reviewed scholarly or scientific journal” (Wikipedia). Examples of lists of preprint servers are available here and here. A list of disciplinary eprint repositories can be found here.

A blog post, The rising tide of preprint servers, provides a brief description of evidence that preprint servers such as  bioRXiv are gaining wider acceptance. One example is provided by the statement (March 24, 2017) by Andy Collings, the Executive Editor of the Open Access journal eLife, that Authors can now submit a preprint to bioRxiv while submitting to eLife.

A short history of preprint servers is available in an article (September 29, 2017) by Jocelyn Kaiser in Science magazine, entitled: Are preprints the future of biology? A survival guide for scientists. It’s mentioned in this article that: “In the 1960s, the National Institutes of Health (NIH) in Bethesda, Maryland, mailed photocopies of draft manuscripts to groups of biologists…”. The project was short-lived. I’ve provided a few details about these Information Exchange Groups (IEGs), and have suggested that  they can be regarded as Predecessors of preprint servers.

My own opinion is that Overlay Journals have a rosy future. For more about Overlay Journals, see: Open journals that piggyback on arXiv gather momentum. I’m not aware of any Overlay Journals in Biology or Medicine, but predict that there will be some (eventually).


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Reviews about Open Access in 2016

The purpose of this post is to highlight two reviews (and an article) about Open Access (OA). The first review is: The year 2016 in open access. Cracks in the mainstream – a subjective review, by Witold Kieńć. Topics include the popularity of Sci-Hub, the fall of the impact factor, and the common roots of OA with the open source movement.

The second review is: Open Access Rewards Passionate Curiosity: 2016 in Review  by Elliot Harmon. It begins by noting, with approval, the OA publication of the first direct detection of gravitational waves. It then continues with comments about some OA-related activities during 2016 by the publishing giant Elsevier. Following a summary of some noteworthy recent OA-oriented issues in the USA, the final paragraph includes this excerpt: “…open access publishing rewards the passionate curiosity of readers and researchers all over the world, regardless of their institutional connections“.

An article that merits attention is: In Montreal, a wee opening in the closed world of science research, by André Picard in The Globe and Mail newspaper. He provides an eloquent report on a pioneering Open Science undertaking that’s being initiated by the Montreal Neurological Institute. Two excerpts from his report:

Is the best way to nurture that process – to accelerate the accumulation of knowledge – to have individual researchers hoard their findings in the hope they will hit paydirt someday, or is it to share discoveries openly to spur others?


In the long run, it’s hard to imagine how people will not benefit more from openness and sharing of knowledge than from secrecy and hoarding of findings

.Comments about these, or other developments in 2016 related to OA, would be appreciated.


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Popular OA topic in December 2015

A popular OA topic in December 2015 was the current status of negotiations between the giant academic publisher Elsevier and the Association of Universities in the Netherlands (VSNU). On December 10, it was announced that the Dutch Universities and Elsevier have reached agreement in principle on Open Access and subscription.

A commentary about this agreement, written by John Bohannon and dated December 11, appeared in Science. An excerpt:

…For no additional charge beyond subscription fees, 30% of research published by Dutch researchers in Elsevier journals will be open access by 2018.

“It’s not the 100% that I hoped for,” says Gerard Meijer, the president of Radboud University in Nijmegen, the Netherlands, and the lead negotiator on the Dutch side. “But this is the future. No one can stop this anymore.”

Several tweets about this deal have appeared in December. One example: From Richard Poynder “In unique deal, Elsevier agrees to make some papers by Dutch authors free”

Another example: From Open Access Top News “Dutch universities and Elsevier reach deal over open access”

There was also a good deal of interest in this tweet: “What If Elsevier and researchers quit playing hide-and-seek?”. For example, from OA Tracking Project

An excerpt from the article linked to in the latter tweet:

Publishing giant Elsevier recently made headlines with its attempts to curb sharing of its papers. When Elsevier persuaded a court to order two websites taken down, they quickly reemerged at different URLs. The story demonstrates what anyone who uses the Internet already knows: copyright lawsuits only temporarily slow sharing. They don’t prevent it.

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Due diligence when invited to join the editorial board of a new OA journal

I’ve received an unsolicited (spam) email informing me that a new open access journal, International Journal of Stem cell Research & Therapy, has been launched. The publisher is  ClinMed International Library (CMIL). I was invited to join the editorial board of the new journal, and to submit an editorial. I’ve refused the invitation.

One should undertake due diligence before joining an editorial board  (or submitting an article) to a journal of this sort. Currently, CMIL publishes 16 journals. At present, the archives of all of these journals are empty. It’s stated in the Open Access section that the journal uses article processing charges (APCs) to cover its costs, but I could find no information about the magnitude of these APCs. I looked for this information in the FAQs section, but it’s empty at present.

In the Guidelines section, it’s stated that: All the articles are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided that the published work is properly cited. This seems to refer to a CC BY license, but this isn’t stated.

Finally, I checked Beall`s List of questionable, scholarly open-access publishers. Yes, CMIL was on the list. The criteria for inclusion of publishers onto Beall`s List are available here.

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Open Access: Sweet Dreams and Nightmares

I’m a supporter of Open Access (OA) and have been for more than a decade. Over that time, the uptake of OA has been encouraging, but rather slow. According to Björk and Hedlund, a reason for this is that established journals and publishers have not had strong enough incentives to change their business models. Year after year, I’ve been hoping that the adoption of OA would reach a tipping point, after which uptake would be very rapid. A pessimistic opinion: although adoption continues to increase, it isn’t obvious that such a tipping point has been reached yet.

For anyone unfamiliar with OA (why are you here?), the OA literature has been defined by Peter Suber as literature that is “digital, online, free of charge, and free of most copyright and licensing restrictions“. OA is sometimes also used to refer to online literature where only price barriers have been removed. Such literature has been termed “gratis OA” by Peter Suber.

There are two main routes to OA, described in the Budapest Open Access Initiative. One is the self-archiving of articles in open electronic archives or repositories (“Green OA“). The other is publication in OA journals (“Gold OA“). There continues to be debate about the relative merits of Green and Gold OA.

A variation on Gold OA is “Hybrid OA“, where only some of the articles are in the journal are OA (after payment of a fee). There are problems with Hybrid OA. A major one is “double dipping”, where libraries are charged for content, even though an article processing fee (APF) has already been paid to make it available OA.

I daydream from time to time about OA. I’ve had some dreams that are sweet, and some that are nightmares. Two examples:

Sweet Dream #1: No embargoes for articles in PubMed Central (PMC).

Embargoed articles in the PMC repository are not immediately free on publication, but only after a specified time period. At present, embargoes of up to one year are permitted by the Public Access Policy of the US National Institutes of Health (NIH). The number of embargoed articles in PMC is not a negligible proportion of the total. For example, on May 27, 2014, a search of PMC was done for the keywords “stem cell”, with limits activated so that embargoed articles were included in the search result. This search yielded 7,187 embargoed articles within a total of 110,156 articles (6.5%).

Mike Taylor, a scientist (palaeontologist), has argued that every manuscript accepted by a publisher should be immediately made freely available with no embargo. His view (March 15, 2013):  “Any publisher that argues against this policy is saying that the value they add is inadequate” (his boldface). For a publisher-oriented contrary view, see: Getting Open Access Embargoes Right: Rational Policy Must Be Evidence-Based. (The comments section of this blog post includes several exchanges between Mike Taylor and those opposed to his argument. They illustrate the difficulties faced by those who seek Green OA without any embargoes).

The number of articles published in credible fully OA journals is accelerating. Such Gold OA journals have the desirable feature that they always provide immediate, unembargoed OA to peer-reviewed research articles. So, if all articles in PMC had been published in Gold OA journals, the percentage of embargoed articles would be zero. Nice dream.

Nightmare #1: Support for PMC is withdrawn.

There has been a series of attempts aimed at reversing the NIH’s Public Access Policy. One illustrative example is the Research Works Act (RWA). It was introduced into the US House of Representatives on December 16, 2011. After much opposition, especially from activist members of the scientific community, support for the RWA was withdrawn on February 27, 2012.

The RWA wasn’t the first attempt to reverse the NIH’s Public Access Policy (see the Wikipedia entry for the RWA). So, one can assume that it won’t be the last. A very bad dream involves a scenario where an attempt to reverse the Public Access Policy finally is successful, and, as a result, PMC ceases to be useful and is no longer supported.

Sweet Dream #2:  The PeerJ business model succeeds and is copied.

Peer J, an OA megajournal launched in 2012, has an innovative business model. Unlike other Gold OA journals that charge an APF, it uses a “pay once, publish for life” business model. There are several publishing plans. A low-cost example is US$99 for one peer-reviewed publication per year. Another is US$299 for unlimited peer-reviewed publications. For articles with multiple authors, only the first 12 authors per paper need to have a paid publishing plan.

Those with paid publishing plans are asked “to contribute one question, comment, or peer review (if qualified) to [PeerJ] every 12 months, or risk their publishing plan lapsing“.

There’s a review, “PeerJ’s $99 open access model one year on” (March 13, 2014) in Times Higher Education (THE). It’s asked in the review “will others go on to ape its low-cost, multi-featured, user-friendly model?“.

If this low-cost Gold OA publication does survive, and develops a widely-recognized, very favorable reputation, then one can dream about this business model being copied. Perhaps a truly competitive market involving low-cost megajournals would develop. Another nice dream.

Nightmare #2: PeerJ is sold to Elsevier and prices rise sharply.

PeerJ isn’t self-sustaining yet (perhaps by 2015 – see the THE article) . If it does succeed in becoming self-sustaining without changing its current prices, then it could become attractive to one of the larger publishers. An example is provided by BioMed Central (BMC), a Gold OA publisher that was founded in 2000. BMC was a pioneer in the successful use of a business model based on article processing fees (APFs). In 2008, BMC was acquired by the large publisher Springer.

It seems possible that the even larger publisher Elsevier might succeed in buying PeerJ. Elsevier could then add PeerJ to its set of OA options. It could also decide to increase the prices for publication in PeerJ. Bad dream.

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Two Different Kinds of Open Access Buttons

The first kind of Open Access (OA) button is the “request eprint” button, built into EPrints institutional repository software (or, the request copy button in DSpace software). This button has also been referred to as the Fair Dealing Button, or the Fair Use Button.

Stevan Harnad has, especially since 1994, been a passionate advocate for OA. He has also repeatedly pointed out the virtues of Green OA, preferably via an Immediate-Deposit/Optional-Access mandate (ID/OA). This mandate is based on the deposition of articles into freely-accessible institutional repositories.

The second kind of button is the recently-launched (November 18, 2013) Open Access Button. It was created by two undergraduates from the U.K. (See: Students Launch “Button” to Put Denied Access to Research on the Map).

This second button should not be confused with the first. The latter button is a browser-based tool that can map who is denied access to a research article. (See: Tracking and mapping the impact of paywalls one click at a time).

The two students are David Carroll and Joseph McArthur. They co-authored an article in which they described their reasons for undertaking this project. The article is: The Open Access Button: It’s time we capture individual moments of paywall injustice and turn them into positive change (published on September 2, 2013).

Does it matter that there’s some ambiguity about the term “OA button”? Probably not. There’s already much confusion about OA, confessed by supporters of OA as well as by non-supporters. See, for example, Open Access Headaches by Stephen Curry (November 3, 2013) and Open Access on the Sea of Confusion by David Wojick (November 11, 2013).

It’s the major policy issues about OA that matter the most. A few more drops of ambiguity in a reservoir of uncertainty seems unlikely to make much difference. The OA policy situation here in Canada is illustrated by: NSERC, SSHRC want feedback on open access. Excerpts: “The major research funding agencies in Canada are looking for feedback on a policy that will require federally-funded research in peer-reviewed journals to be freely available to the public within one year of publication” and “The Tri-agency Open Access Policy is modelled after the open access policy at the Canadian Institutes of Health Research, which went into effect in 2008“.

Disclosure: During 2006-2007, I chaired the Advisory Committee on Access to Research Outputs of the Canadian Institutes of Health Research (CIHR). Amendments were made, effective January 1, 2013, to the CIHR Open Access Policy, formerly known as the Policy on Access to Research Outputs. (It’s the Governing Council of the CIHR that decides policy, not an advisory committee).

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How to select an Open Access journal?


I was recently asked by a colleague about Open Access (OA) journals. Her interests are in the areas of cancer and medical genetics. She’d had unfortunate recent experiences with anonymous peer review, and wished to find a suitable OA journal that uses open peer review – with: a)  identification of the reviewers, and b) publication of their reviews.

After responding with a few suggestions, I subsequently thought that a somewhat more extensive exploration of selected relevant  journals might be of wider interest.

If one isn’t very familiar with OA journals, then one needs to be cautious about selecting one. For authors in the biomedical area, it’s preferable that the journal be indexed in PubMed, the widely-used bibliographic database. A convenient way to check this is to enter the full name of the journal into the PubMed Single Citation Matcher.

Another valuable source of information is the Directory of Open Access Journals (DOAJ), which “aims to be comprehensive and cover all open access scientific and scholarly journals that use a quality control system to guarantee the content“. Although the DOAJ includes information about over 9,000 OA journals, it’s able to provide only a very limited amount of information about each one.

A useful listing of cancer-related journals is the Oncology, cancer research section of the Free medical journals site. While many of these journals permit immediate free access, some only permit embargoed access.

I’ve put together some information about a selected set of 15 OA journals. The focus is mainly, but not entirely, on ones that will consider articles about medical genetics and/or cancer. A few provide open peer review. Of these, two that I suggested to my colleague were #1 (BMC Medicine) and #3 (BMJ Open).

Journal Characteristics

The 15 journals are not listed in any rank order. Individual authors will give different weights to the particular characteristics of each journal. The primary aim of this post is to highlight some of these characteristics.

For example, if the cost of the Article Processing Fee (APF) is a major consideration, then the new journals #4 (eLife, no APF at present) and #5 (PeerJ, no APF; memberships instead) merit attention. If, on the other hand, the journal’s Impact Factor (JIF) is a major consideration, then longer-established journals such as #10 (PLOS Medicine, JIF=16.27), #8 (PLOS Biology, JIF=11.45) or #7 (The EMBO Journal, JIF=9.205) are possibilities.

Another consideration is Article-Level Metrics (ALMs). ALMs are an attempt to measure impact at the article level using traditional and emerging data sources. These emerging data sources are often called altmetrics. There are well-known concerns about the various uses of the Impact Factor of a journal, especially when it’s used as a surrogate measure of the quality of individual articles in a journal (see also: Journal impact factor: a brief review). ALMs are intended to provide more meaningful measures of the impact of individual articles. At present, there are a variety of approaches designed to provide ALMs. None of them has, as yet, achieved market dominance.

Finally, there’s the issue of the licence used to specify usage rights. All of the 15 journals listed below use Creative Commons licences. Most use the Attribution (CC-BY) licence. The EMBO Journal (#7) permits authors to choose one of three Creative Commons licences, including CC-BY. The CC-BY licence is the most permissive one. See: Author licence agreement.


Some of the major publishers are represented in the list of 15 journals. They include BioMed Central, BMJ Group, Nature Publishing Group, Public Library of Science (PLOS), Frontiers and Hindawi Publishing Corp. For a much longer list of publishers, see the Members of the Open Access Scholarly  Publishers Association (OASPA). One of the roles of OASPA is to promote “Gold” OA journals of the kind considered in this post. As noted in a footnote on the Mission and Purpose section of the OASPA website, “Gold OA refers to implementing the free and open dissemination of original scholarship by publishers, as opposed to Green OA, in which free and open dissemination is achieved by archiving and making freely available copies of scholarly publications that may or may not have been previously published“.

For information about the restrictions that various publishers place on Green OA, visit the SHERPA/RoMEO database of publishers’ policies on copyright and self-archiving.


The 15 OA journals considered here are listed below. Which one would I choose for an article of my own? If there were co-authors, I’d need to take their preferences into account. If not, and the article was in the cancer and/or genetics area, I’d probably try #5 (PeerJ), mainly because it has innovative membership plans, provides ALMs, and publishes (anonymous) reviewers’ comments.

The Selected Journals

#1) BMC Medicine:
Scope: Original research, commentaries and reviews that are either of significant interest to all areas of medicine and clinical practice, or provide key translational or clinical advances in a specific field.
Journal Impact Factor (JIF): 6.035
Article Processing Fee (APF): £1515/€1785/US$2325. See:
Licence: Creative Commons CC-BY (must attribute the work).
Article-Level Metrics: Via (see: “About this article” under the “Associated Material” in the right-hand column that’s shown for each published article). An example:
Peer Review: Reviewers are named and reviewers’ reports are published. An example:

#2) BMC Medical Genetics:
Scope: Considers articles on the effects of genetic variation in individuals, families and among populations in relation to human health and disease.
JIF: 2.33
APF: £1290/€1520/US$1980. See: Article Processing Charge FAQ #3.
Licence: CC-BY
Article-level metrics: Via (see “About this article”, as described above for BMC Medicine).
Peer Review: Reviewers are named and reviewers’ reports are published. An example:

#3) BMJ Open:
Scope: Publishes medical research from all disciplines and therapeutic areas.
JIF: Currently being tracked for its first JIF. [Announced June 20, 2013: First JIF is 1.58].
APF: £1350. See:
Licence: The default licence is CC-BY-NC (Attribution-NonCommercial), but where the funder requires it the author can select CC-BY. See: Compliance with Funders Open Access policies.
Article-level metrics: Article Usage Statistics are provided. An example:
Peer Review: Reviewers are named and reviewers’ comments are published. An example is available [PDF].

#4) eLife:
Scope: From basic biological research through to applied, translational and clinical studies.
JIF: No JIF yet. New journal, launched in 2012.
APF: Free of charge, at least for an initial period. Supported by the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust.
Licence: CC-BY
Article-level metrics: Number of views, PDF downloads and XML downloads are provided for each article.
Peer Review: The decision letter from the editor and the author response are published, if author agrees. An example: (look under “Jump to” in the right-hand column).

#5) PeerJ:
Scope: Research Articles in the biological and medical sciences.
JIF: No JIF yet. New journal, launched in 2013.
APF: No APF. Uses membership plans instead.
Licence: CC-BY
Article-level metrics: Via ImpactStory.
Peer Review: Reviewers may be anonymous but reviewers’ comments are published, if author agrees. An example:

#6) Biology Direct:
Scope: Genomics, Bioinformatics and Systems Biology; Immunology; Mathematical Biology.
JIF: 4.02
APF: £1290/ €1520/US$1980. See: Article-processing charges FAQ #3.
Licence: CC-BY
Article-level metrics: Via
Peer Review: Reviewers are named and reviewers’ reports are published. A commentary about open review in Biology Direct is available here. An example:

#7) The EMBO Journal:
Scope: Original research of general rather than specialist interest in molecular biology and related areas.
JIF: 9.205
APF: $3,900 (for Hybrid Open Access, via EMBO Open). Total charges include page charges, in addition to the APF.
Licence: Open articles are published under one of three Creative Commons licences at the free choice of the authors. See: Who retains copyright of EMBO Open articles?
Article-level metrics: Citation data from Scopus are provided for articles that have been cited at least once.
Peer Review: Reviewers are anonymous, but reviewer’s reports are published. An example is available [PDF].

#8) PLOS Biology:
Scope: Claims to feature works of exceptional significance, originality, and relevance in all areas of biological science.
JIF: 11.45
APF: US$2900. See: Publication Fees.
Licence: CC-BY
Article-level metrics: An Article-Level Metrics Suite is provided.
Peer Review: Reviewers can choose to be anonymous. No reviewer reports are published.

#9) PLOS Genetics:
Scope: A forum for the publication of articles of broad interest to the genetics and genomics community.
JIF: 8.69
APF: US$2250. See: Publication Fees.
Licence: CC-BY
Article-level metrics: An Article-Level Metrics Suite is provided.
Peer Review: Reviewers can choose to be anonymous. No reviewer reports are published.

#10) PLOS Medicine:
Scope: Outstanding research and commentary on the major challenges to human health worldwide.
JIF: 16.27
APF: US$2900. See: Publication Fees.
Licence: CC-BY
Article-level metrics: An Article-Level Metrics Suite is provided.
Peer Review: Reviewers can choose to be anonymous. No reviewer reports are published.

#11) PLOS ONE:
Scope: Designed to communicate primary scientific research, in any discipline that will contribute to the base of scientific knowledge.
JIF: 4.09
APF: US$1350. See: Publication Fees.
Licence: CC-BY
Article-level metrics: An Article-Level Metrics Suite is provided.
Peer Review: Reviewers can choose to be anonymous. No reviewer reports are published.

#12) Frontiers in Cancer Genetics:
Scope: Ranges from whole genome to focused studies of individual genes and molecular pathways.
JIF: No JIF yet.
APF: €1,600 for regular submission of original research articles. See: Fees.
Licence: CC-BY
Article-level metrics: Via
Peer Review: Review editors and reviewers are identified on accepted articles. No reviewer reports are published.

#13) F1000Research:
Scope: All articles, including research findings, analyses of scientific developments, opinions, and comments are published immediately, following a quick internal check for obvious inappropriateness.
JIF: No JIF yet. New journal, launched in 2012.
APF: US$1000 for research articles. See: Article Processing Charges.
Licence: CC-BY
Article-level metrics: Number of views, PDF downloads and XML downloads are provided for each article.
Peer Review is post-publication. Reviewers are named and short reviewer reports are published. Articles that pass post-publication peer review will be indexed by PubMed. At present, this indexing hasn’t begun yet. See some critical comments here.

#14) Genetics Research International:
Scope: Publishes original research articles, review articles, and clinical studies in all areas of genetics.
JIF: No JIF yet. Began publishing in 2011.
APF: Free during May 2013. See: Article Processing Charges.
Licence: CC-BY
Article-level metrics: Not yet available.
Peer Review: Anonymous peer review.

#15) Journal of Cancer Research:
Scope: Publishes original research articles, review articles, and clinical studies in all areas of cancer research.
JIF: No JIF yet. New journal, very recently launched.
APF: US$600. See: Article Processing Charges.
Licence: CC-BY
Article-level metrics: Not yet available.
Peer Review: Anonymous peer review.

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