2019 In Review

2019 Was Big for Academic Publishing. Here’s Our Year in Review is an article by Diana Kwon in TheScientist on December 27, 2019. Some of the OA-related issues that are reviewed include:

  1.  A brief mention of “concerns about the presence of predatory journals on PubMed”.
  2.  A brief mention of a trend toward “more scientists are opting to deposit their [supplementary] files into online repositories hosted by universities, research institutions, and companies“.
  3.  A section entitled: “UC breaks with Elsevier“. The University of California (UC) has tried to obtain, from Elsevier, “a contract that combines subscriptions to read paywalled journals and publishing in open-access formats into a single fee“. So far, this effort has been unsuccessful. Since July 2019, those at UC have been unable to access new articles published in Elsevier’s paywalled journals.
  4. In the next section, entitled “Deals are Made, three deals are noted that do support publication of OA articles, as well as provide access to paywalled papers, all for a single annual fee. These deals are between Wiley and academic consortia in Germany, Norway and Hungary, Deals that involve OA elements are often called “transformative”, Publishers other than Wiley have made transformative deals, even including (more recently) Elsevier, which appears to have become more flexible.
  5. In a final section, entitled “Changes to Plan S”, the current status of Plan S is reviewed. One of the noteworthy changes is “a softened stance on hybrid journals—they will now be allowed for a limited time if they are a part of a transformative agreement“.

This review provides an excellent summary of noteworthy OA-related developments that happened in 2019.


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Plan S, a Work in Progress

Plan S is a controversial European initiative designed to revolutionize scholarly publishing. As summarized by Anette Breindl:

“Plan S mandates that starting in 2020, scientists funded by the national agencies or research councils of 11 nations – Austria, Britain, France, Ireland, Italy, Luxembourg, the Netherlands, Norway, Poland, Slovenia and, partially, Sweden – will have to publish their research open-access immediately. (The U.S. NIH has been mandating that NIH-funded research be open-access six months after they are first published.)”.

The Wikipedia entry for Plan S provides detailed information about the initiative.

Tony Ross has provided Thoughts on Plan S implementation guidelines. He suggests several issues about which futher clarification is needed.

Koen Hufkens has authored critique of objections to Plan S. Some controversial aspects of Plan S are addressed.

Concerns about Plan S from the perspective of a commentator from the Global South are discussed here.

Concerns from the perspective of Society Publishers are described here.

Diana Kwon, in an article in The Scientist dated December 19, 2018, presented a perspective on Plan S that included a paragraph entitled “A work in progress“. It can be fearlessly predicted that there will be more progress in relation to Plan S in 2019.

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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” https://twitter.com/RickyPo/status/675606958624415744

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 https://twitter.com/oatp/status/677894862717358080

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: http://www.biomedcentral.com/bmcmed
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:  http://www.biomedcentral.com/bmcmed/about/apcfaq/howmuch
Licence: Creative Commons CC-BY (must attribute the work).
Article-Level Metrics: Via Altmetric.com (see: “About this article” under the “Associated Material” in the right-hand column that’s shown for each published article). An example: http://www.biomedcentral.com/1741-7015/11/124/about
Peer Review: Reviewers are named and reviewers’ reports are published. An example: http://www.biomedcentral.com/1741-7015/11/3/prepub

#2) BMC Medical Genetics: http://www.biomedcentral.com/bmcmedgenet
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 Altmetric.com (see “About this article”, as described above for BMC Medicine).
Peer Review: Reviewers are named and reviewers’ reports are published. An example: http://www.biomedcentral.com/1741-7015/11/106/prepub

#3) BMJ Open: http://bmjopen.bmj.com/
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: http://bmjopen.bmj.com/site/about/faqs.xhtml#11
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: http://bmjopen.bmj.com/articleusage?rid=3/3/e002114
Peer Review: Reviewers are named and reviewers’ comments are published. An example is available [PDF].

#4) eLife: http://elife.elifesciences.org/
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: http://elife.elifesciences.org/content/2/e00499 (look under “Jump to” in the right-hand column).

#5) PeerJ: https://peerj.com/
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: https://peerj.com/reviews/68/

#6) Biology Direct: http://www.biology-direct.com/
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 Altmetric.com.
Peer Review: Reviewers are named and reviewers’ reports are published. A commentary about open review in Biology Direct is available here. An example: http://www.biology-direct.com/content/8/1/3#sec5

#7) The EMBO Journal: http://www.nature.com/emboj/index.html
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: http://www.plosbiology.org/
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: http://www.plosgenetics.org/
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: http://www.plosmedicine.org/
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: http://www.plosone.org/
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: http://www.frontiersin.org/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 Altmetric.com.
Peer Review: Review editors and reviewers are identified on accepted articles. No reviewer reports are published.

#13) F1000Research: http://f1000research.com/
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: http://www.hindawi.com/journals/gri/
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: http://www.hindawi.com/journals/jcr/
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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Open access – is the UK leading the way?

Novel scientific findings are disseminated via scientific journals. Currently, the scholarly publishing system has become dysfunctional and is in turmoil. The main reason is that the system was designed for the era of paper and print, not for the digital era.

For those involved in scientific publishing, the ‘ancient Chinese curse’ (more likely recent and Western) comes to mind: “May you live in interesting times“. The purpose of this post is to outline some relevant aspects of these ‘interesting times’, and to highlight some recent contributions made by the UK to the ‘Open Access Movement’. This OA Movement is increasingly seen as a solution to the currently-dysfunctional publishing system.

Some History

Scientific journals have a long history. The first scientific journal in English was the Philosophical Transactions of the Royal Society (Phil Trans), published in March of 1665 by the Royal Society of London. It was the first journal in the world exclusively devoted to science. It is still being published today, making it also the world’s longest-running scientific journal.

Thus, it was in London that scientific journals began. There was another academic journal that began publication, in January of 1665, in Paris. Later renamed Journal des Savants, it was more news-oriented than Phil Trans, was not restricted to scientific news, and subsequently became more of a literary journal.

The purpose of Phil Trans was to inform the Fellows of the Society and other interested readers of the latest scientific discoveries. But it accomplished much more, as described by Jean-Claude Guédon in an article, In Oldenburg’s Long Shadow, published in 2007. Phil Trans not only permitted scientists to communicate their discoveries and share knowledge. It also served as a public record of original contributions to scientific knowledge. In this way, it served as a public registry of intellectual property.

Such a registry meant that it was no longer necessary to use other (sometimes unorthodox) methods to ensure intellectual priority to the discoveries or insights of scientists. For example, J-C Guédon comments that Galileo had sent an anagram of the phrase describing his discovery of Jupiter’s satellites to Kepler (and to many others) in order to establish his priority. Phil Trans made such ingenious strategies unnecessary.

The founding editor of Phil Trans was the first secretary of the Royal Society, Henry Oldenburg. Oldenburg began the practice of peer review – sending submitted manuscripts to experts who could judge their quality before publication. Pre-publication peer review continues to be a feature of scholarly journals. Thus, a key feature of scholarly publications also originated in London.

Transition Toward Open Access

Now, after almost 350 years of existence, scientific journals are in the process of undergoing a major transition. The transition is away from journals being subscription-based, where the reader must pay a toll in order to have access, toward Open Access (OA), where no toll needs to be paid.

OA is the practice of providing unrestricted access via the Internet to peer-reviewed scholarly journal articles. It’s the existence of the Internet that’s made OA feasible. Scholarly publishing is being reconstructed to adapt it to the Internet age, where the costs of distribution of electronic versions of articles are much less than the costs of distributing paper versions.

OA comes in two degrees. A distinction needs to be made between Gratis and Libre OA. Some OA literature is already digital, online and free of charge (Gratis OA). Some is not only free of charge, but also free of most copyright and licensing restrictions (Libre OA). A long-term goal of the open access movement is to foster the transition of as much as possible of the scholarly literature from toll access (TA) to Libre OA.

At present, there is an ongoing debate about how best to achieve this goal. The main debate is about the best balance between ‘Green’ OA and ‘Gold’ OA. Green OA is based on OA repositories. OA repositories do not perform peer review. Instead, they provide a venue for articles that have been peer-reviewed elsewhere. Gold OA is based on OA journals that do perform peer review. Peter Suber (in 2008)  emphasized that the Gratis/Libre distinction (see above) is not synonymous with the Green/Gold distinction.

A recurring criticism of OA is that it will lead to the traditional peer review process being abandoned. However, this criticism is factually inaccurate.

Gold OA Journals

The UK-based BMJ (formerly, the British Medical Journal) became, in 1998, the first major general medical journal to provide OA to its research articles. It also began to deposit the full text in the PubMed Central (PMC) repository, and to allow authors to retain the copyright of their articles. BMJ pioneered OA medical research articles. Non-research articles in BMJ ceased to be OA in 2005 (see Comments section here).

Another of the first OA journals in medicine, the Journal of Medical Internet Research (JMIR), published its first issue in 1999. JMIR is based in Canada. It’s a Gold OA journal that’s now the leading journal in Medical Informatics.

Some examples of early OA publishers are listed here and here.

The first of the large for-profit STM (Science, Technology and Medicine) OA publishers was BioMed Central (BMC), founded in the UK in 2000. Hence, a UK-based publisher was a pioneer in the establishment of Gold OA as a viable publishing option for a commercial publisher. In October of 2008, BMC was acquired by Springer, the 2nd largest STM publisher. BMC currently publishes over 200 peer-reviewed OA journals.

Another pioneering OA publisher is Public Library of Science (PLoS), which launched it’s first journal in 2003. It currently publishes seven peer-reviewed journals.

An increasing number of toll-access journals offer a hybrid OA option. Upon payment of a publication fee, individual articles are made OA. This provides two revenue streams to the publishers of hybrid OA journals, one from subscriptions, and one from publication fees.

The hybrid OA model has led to concerns that publishers may be “double-dipping”, because they receive the Article Processing Charges (APCs) but do not reduce subscription fees.  Royal Society Publishing provides one recent example of a publisher of hybrid OA journals that has promised to implement a transparent pricing policy. As has been pointed out by Stuart Shieber, it’s difficult to determine whether or not double-dipping is happening.

Costs of Gold OA

Of course, the publication of articles involves costs. Gold OA does away with the use of subscriptions to cover these costs. Instead, there are a variety of other ways to cover the costs of publication. The description of each journal listed in the Directory of Open Access Journals (DOAJ) includes information about whether or not a publication fee is charged. Many of the journals listed in the DOAJ do not have APCs.

Also, OA journals that do have APCs commonly offer a fee waiver for authors with limited financial resources. Examples are the waivers offered by PLoS  and by Frontiers.

However, within the biomedical sciences, the prevalent approach of publishers is to require the authors (or their funding agencies or institutions) to pay an upfront APC for Gold OA. For example, in 2002, BioMed Central’s business model evolved to include APCs, and these have been BMC’s primary source of revenue since then,

A major advantage of Gold OA is that articles are publicly accessible immediately upon publication. A major disadvantage is that the APCs can be costly. At the high end is Cell Reports (Cell Press), where the APC is US$5000.

The APC for Open Biology (Royal Society Publishing) is much lower, at US$1932, and is currently being waived. The APC for the very popular journal PLoS ONE (Public Library of Science) is even lower, at US$1350.  A recently-launched (2011) journal that’s analogous to PLoS ONE is Scientific Reports (Nature Publishing Group). Its APC is also US$1350. A comparison of APCs has been provided by the OA publisher BioMed Central. The APCs of BMC itself are in the £1075-£1230 (approx. US$1665-$1905) range.

A list of Publishers with Paid Options for Open Access (publishers that provide hybrid OA) is available via the SHERPA/RoMEO website, but the list and the information about APCs may not be up-to-date. Nature Communications (Nature Publishing Group) is at the high end (US$5000 per article). The hybrid OA option of Royal Society Publishing (US$2380) is less expensive.

A novel approach to OA publishing is the new journal eLife. It is supported by three influential research funders, the Wellcome Trust in the UK, the Howard Hughes Medical Institute in the USA, and the Max Planck Society in Germany. It will begin publication in the winter of 2012-13. The APC for eLife has not yet been announced, but will be waived while the journal is being established.

An even more novel approach is being used by PeerJ, a new OA publication that will be open for submissions in the last quarter of 2012. PeerJ will not depend on either subscriptions or APCs as sources of funding. Instead, every author must have a membership plan in order to publish in PeerJ. The plan is good for the life of the author, so long as the author meets a requirement to submit a review at least once per year.

One could regard the PeerJ membership payment as a one-time-only submission fee. Pricing of the membership  ranges from US$99 (one publication per year) to US$299 (unlimited publications per year). If a manuscript has more than 12 authors, then only 12 authors need to have a paid membership plan.

All of the journals mentioned above provide Gratis OA. Not all provide Libre OA. One needs to look at whether or not a Creative Commons Attribution License (CC-BY) is being used. CC-BY is the most accommodating of the Creative Commons copyright licenses and provides Libre OA.

Green OA Via OA Repositories

Green OA requires that the authors deposit their works in OA repositories. A pioneering OA repository for electronic prepublications of scientific articles was ArXiv, established at Los Alamos National Laboratory in the USA in 1991 (it moved to Cornell University in 2001). ArXiv provides public access to e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. The e-prints are not peer reviewed, but moderators review submissions and may reject or recategorize any that are deemed inappropriate or off-topic.

In 2000, PubMed Central (PMC) began operation. An examination of it’s history shows that the ArXiv was the primary conceptual model for what became PubMed Central. PMC is a free full-text archive of biomedical and life sciences journal literature. It’s sponsored by the US National Institutes of Health (NIH).

PMC International currently supports UKPMC (operational in 2007; will become Europe PMC in November 2012) and PMC Canada (operational in 2009). UKPMC was the first participant in PMC International, and the change in name of UKPMC is in recognition that the European Research Council (ERC) will be the third European funder to join UKPMC.

PMC is, in part, a national repository that captures the output of publicly funded research (especially, research supported by the NIH). The Public Access Policy of the NIH, implemented in 2008, requires that final peer-reviewed journal manuscripts that arise from NIH funds be accessible to the public on PMC no later than 12 months after publication.

There are other kinds of repositories, including many institutional repositories. The Directory of Open Access Repositories (OpenDOAR) and the Registry of Open Access Repositories (ROAR) list over 2000 research institutional or departmental OA repositories worldwide.

A major advantage of Green OA is that it costs authors nothing to self-archive an article in an OA repository, if a suitable one is available. There are no submission fees. A disadvantage is that there is much variation across different journals in their restrictions on Green OA. A useful database of the policies of various journals is available at the SHERPA/RoMEO website. For example, Nature permits the author’s version of an accepted paper (the unedited manuscript) to be archived in PMC and/or in the author’s institutional repository, for public release six months after publication. Such embargoes on public access are a major drawback of Green OA.

Although there is an ongoing debate about the optimal balance between Gold and Green OA, policy decisions are being made about how best to foster the transition from TA to OA (see below).

Political Appeal of OA

Various observers describe today’s global economy as one in transition to a “knowledge economy,” as an extension of an “information society.” In the UK, David Willetts, the Minister of State for Universities and Science, has articulated a vision of a knowledge economy supported by OA – to provide public access to publicly funded research results. In a speech made on 2 May 2012 to the Publishers Association annual general meeting in London, he said:

The evidence underpinning our ambition for public access is compelling. For example, publicly funded and freely available information from the Human Genome Project led to greater take up of knowledge and commercialisation than from earlier protected data. To date, in fact, every dollar of federal investment in the Human Genome Project has helped generate $141 for the US economy. Separately, a report this year from the US Committee for Economic Development has concluded that the US National Institute of Health’s policy of open access after one year has accelerated scientific progress and the transition from basic research to commercialisation; generated more follow-on research and more citations; and reduced duplicate or dead-end lines of inquiry – so increasing the US government’s return on its investment in research. The researcher Philip Davis, meanwhile, has found that when publishers randomly made certain articles open access on journal websites, readership increased by up to 250% compared to protected articles.

Thus, David Willetts emphasized the economic impact of the Human Genome Project,  highlighted information provided in a 2012 report [PDF] about the Public Access Policy of the US National Institutes of Health (NIH) , and referred to the relevant work of Philip Davis.

The Finch Report

In October of 2011, David Willetts had already set up the Working Group on Expanding Access to Published Research Findings (‘Finch Group’). It was chaired by Dame Janet Finch DBE, Professor of Sociology at Manchester University and independent co-Chair of the Council for Science and Technology. The Group’s role was to examine how UK-funded research findings could be made more accessible.

The membership of the Group, 16 in all, included OA advocates and other interested  parties. The latter included representatives of large commercial for-profit publishers (Springer, Wiley Blackwell). The presence of these representatives took into account the fact that the UK is home to a vigorous academic and scholarly publishing industry. Did these representatives drive the policy direction taken by the Group? It seems more likely that the publishing industry is in ferment, and that the representatives of publishers were not in a position of strength.

The report from the Finch Group (the Finch Report) was published on June 18, 2012. On July 16, 2012, there were three major announcements that signaled a transformation of OA policy in the UK. Firstly, the UK government announced that it had accepted the recommendations included in the Finch Report, and plans to have better access to British scientific research and academic papers by 2014. Secondly, the Research Councils UK (RCUK) announced a new OA policy, applicable to all qualifying publications being submitted for publication from April 1, 2013. Thirdly, the Higher Education Funding Council for England (HEFCE) announced plans to make publicly-funded research more freely available after 2014.

As Peter Suber has pointed out in an editorial in BMJ, “These announcements signal a massive shift towards open access for publicly funded research in the UK…“. In a much longer essay, Tectonic movements toward OA in the UK and Europe, he has analyzed this “massive shift” in a very thorough way.

Gold OA Preferred Over Green OA

The Finch Group expressed a strong preference for Gold OA over Green OA. According to a clarification of the RCUK policy, in comparison with the Finch Report, RCUK also prefers Gold OA, but, if a suitable Gold OA option isn’t available, will accept Green OA, with an embargo of no more than 6 months for science papers (12 months for papers in the humanities and social sciences).

The main concern about the preference for Gold OA expressed by the Finch Group and the RCUK is that a transition to Gold OA, without taking full advantage of Green OA, is needlessly expensive (see, for example, Open Access Evangelism and Key Questions for Open Access Policy in the UK).

On September 7, 2012, the UK government announced that it will provide an extra £10 million to help to cover these transitional costs. A sentence from the announcement: “The investment will be made to 30 institutions receiving funding through Research Councils and UK higher education funding councils“.

The extra £10 million will apparently be a one-off transfer of money from elsewhere in the science budget. The RCUK announcement includes plans to provide block grants to support payment of APCs. Any additional funds that may be needed must come out of the already-stretched budgets of funding agencies and universities.

One of the key benefits of OA, from the perspective of the RCUK, is “the potential it offers to the research community (and beyond) to mash, mine and mix information and knowledge.  This provides real opportunities to substantially further the progress of research and innovation“. Libre OA is required if this potential is to be fully realized. This is a reason why the Finch Group and the RCUK have endorsed Gold OA and a CC-BY copyright license.

What’s Next?

Will other countries join the UK in its efforts to implement a transition to Gold OA? An answer came quickly. On July 17, 2012 – only one day after the announcements in the UK – the European Commission announced that, as of 2014, all scientific publications produced with funding from Horizon 2020 will have to be OA. Horizon 2020 is the EU’s Research & Innovation funding program for 2014-2020. Apparently, equal weight will be given to Gold and Green OA.

The Reputation Issue

Studies of authors’ views about factors that influence their choice of a journal as a venue for publication have identified journal reputation as a major factor (see, for example, here and here). A very widely used indicator of a journal’s reputation is it’s Impact Factor, which is the average number of citations received per paper published in that journal during the two preceding years. There have been many criticisms of the Journal Impact Factor (see: Sick of Impact Factors and Impact Factors: Use and Abuse). A problem for Gold OA journals is that few are more than a decade old. Time is required for a journal to develop a very favorable reputation.

In the age of blogs and social networks, it’s the impact of the article itself, not its venue, that needs to be assessed. Alternative metrics (‘altmetrics‘) are under development.


Will the ‘Reputation Issue’ pose problems about compliance with these new policies in the UK and Europe? The Wellcome Trust (a charitable foundation in the UK that supports biomedical research) has had concerns about compliance with its own OA policy. On June 28, 2012, it announced that it will be tightening up enforcement of the OA policy.

One of the three steps included in the strengthened policy is that Wellcome-funded researchers must be compliant with the Trust’s OA policy before any funding renewals or new grant awards will be activated. Again, it seems likely that a policy initiative that has originated in the UK may serve as a model for other funding agencies, beyond the UK as well as within it.

Sir Mark Walport, director of Wellcome Trust and a champion of OA, has been appointed to take over as UK Government Chief Scientific Adviser in April 2013.

What About the USA?

As noted above, the NIH already has a Public Access Policy. The rate of compliance with this policy currently stands at a respectable 75%. However, a lengthy embargo period of up to 12 months is permitted.

In May, 2012 a petition was created, on a White House website, to advocate implementation of OA policies for all US federal agencies that fund scientific research. The petition has obtained over 30,000 signatures, more than the threshold of 25,000 required to evoke an official response. So far, there’s been no response. The response, Heather Joseph has said, “could be as weak as a simple acknowledgement, or as strong as a policy statement or directive“.

The timing of the petition was no accident. The bipartisan Federal Research Public Access Act (FRPAA) was reintroduced into the Senate (S 2096) and the House (HR 4004) in 2012. FRPAA proposes to extend the NIH policy to other federal agencies, and to shorten the permitted embargo from twelve months to six. A FAQ about FRPAA has been provided by the Alliance for Taxpayer Access.

There has been strong opposition to FRPAA from journal publishers. A main point of opposition is the proposed reduction of the duration of the permitted embargo from 12 months to 6 months.

The House and Senate bills have been referred to committee, and no prompt action seems likely.

Is the UK leading the way during the transition from TA to OA?

The short answer to this question is, I think, “At present, yes”. The announcements in July (see the section on the “Finch Report”, above) have been identified by Bernstein Research, in a very substantial report (PDF) dated September 10, 2012 as “the revival of OA“. I agree.

Will this initiative be successful? Stevan Harnad is a long-time advocate of emphasizing Green over Gold OA during the transition period. He has predicted that, if the RCUK policy isn’t modified, “the UK will lose its historic leadership of the global open access movement along with a good deal of public money that could have been spent on supporting more research…”.

The policy leadership provided by the July announcements was a surprise. It’s a bold attempt to achieve Libre OA  within a very few years. In Stephen Curry on Open Access, post-Finch, dated August 20, 2012, Stephen Curry is quoted as saying (in part):

I have the sense that things are less up in the air now, because the UK has nailed its colors to the mast, but it depends if their policy will win the heart and mind of the scientific community.

In Conclusion

The only prediction that I’m willing to make is that there will be further surprises.

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