Posts Tagged Gold OA

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.


Comments (5)

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.

Comments (13)

Important contributions to OA in Europe

There have been some noteworthy contributions to the Open Access (OA) movement in Europe over the past week.

1) In the UK, the government announced that all UK-funded research will be OA within two years. An interesting commentary about this announcement has been provided by Mike Taylor, accessible via the link in his tweet:

2) The Research Councils UK (RCUK) has strengthened its OA policy, summarized here. The announcement is available via the link in this tweet:

3) The the European Commission (EC) has backed calls for OA. See:


4) The European Research Council (ERC) has announced that it will participate in the UK PubMed Central (UKPMC) OA repository service, and that the repository will be rebranded as “Europe PMC” by 1 November 2012. A link to information about this announcement is included in this tweet:

Comment: Will these important contributions to the OA movement give rise to analogous contributions in other nations? I hope so.

Comments (1)

OGI Genomics Publication Fund

The Genomics Publication Fund (GPF) of the Ontario Genomics Institute was launched on May 19, 2010. Examples of news items about the launch are available via: [PharmaLive][Connotea][BOAI Forum][FriendFeed][GenOmics][GHBN][Bio Saga]. The first paragraph of the OGI news release:

The Ontario Genomics Institute (OGI) has announced the launch of a new fund to support free and unrestricted access to scholarly research papers on genomics published in high impact journals. The OGI Genomics Publication Fund (GPF) will contribute up to $3,000 per publication to genomics researchers in Ontario wishing to make their papers available as Open Access from the earliest date of publication.

Excerpt from the Charter section of the GPF Charter & Guidelines [PDF]:

The Ontario Genomics Institute (OGI) aims to increase the profile, visibility, and citations of genomics research conducted in Ontario and published in top international journals.

At the end of part IV of the Guidelines section of the Charter & Guidelines is a list of recommend journals. The list of “Journals that are Immediately Open Access with no additional open access charge” includes Brit Med J and J Clin Invest, together with five PLoS journals (including PLoS ONE). Lists are also provided of ten “Journals that charge a fee to make an article Open Access” and over 80 “Journals that cannot be made open access unless with specific editorial approval“.


I’ve had one meeting (and a few email exchanges) with OGI staff about the GPF, and am quoted (accurately) in the news release: “This fund is the first of its kind in targeting potential high impact publications”.

The GPF has a focus on Gold OA. However, OGI staff are aware of Green OA, and on page 2 (Step 4) of the Charter & Guidelines, it’s stated that: “Once the accepted manuscript is published the applicant must ensure that the publication is available via PubMed Central or an alternative open access repository …”.

The news release also includes a link to A Very Brief Introduction to Open Access. The author of this concise introduction, Peter Suber, pointed out that: “There are two primary vehicles for delivering OA to research articles: OA journals and OA archives or repositories.” Hybrid OA isn’t explicitly mentioned in this introduction. Perhaps this is because the number of publishers that offer a hybrid OA option has increased considerably since late December, 2004, when this brief version (of a much longer Open Access Overview) was first put online.

The focus on high impact journals limits the options available to those who intend to apply for funds from the GPF. One may ask: which journals are frequently selected for publications related to genomics or proteomics? A preliminary answer to this question can be obtained via PubMed PubReMiner (this resource was found via a comment posted by Brad Bixby to the ResearchGATE Science 2.0 & Publication 2.0 Group, May 14, 2010).

Search #1 used the query: “GENOMICS[TIAB] 2010/01/01:2010/05/01 [DP]” (without the quotes). The search was restricted to the time period between Jan. 1, 2010 and May 1, 2010 in order to limit the number of references assessed. The top ten journals identified (in 727 references) included only two that were on the GPF’s list of preferred journals – Proc Natl Acad Sci USA (#6) and PLoS ONE (#7). The journal ranked #1 was BMC Genomics (an OA journal with a 2008 Journal Impact Factor of 3.9).

Search #2 used the query: “PROTEOMICS[TIAB] 2010/01/01:2010/05/01 [DP]” (again, without the quotes, and for the same time period). The top ten journals identified (in 929 references) included only one that was on the GPF’s list of preferred journals: Mol Cell Proteomics (#3). The journal ranked #1 was Proteomics (a Wiley journal that has an “OnlineOpen” hybrid OA option and a 2008 Journal Impact Factor of 4.6).

These preliminary searches (and similar ones carried out to identify Informatics or Bioethics journals) clearly revealed the need for an assessment of applications to the GPF on a case-by-case basis. The OGI intends to do this. An excerpt from the Journals section at the end of the Charter & Guidelines [PDF]:

Manuscripts accepted in a journal listed below or with an ISI impact factor above 8 will be considered by OGI for funding via the GPF. For manuscripts accepted by other journals the applicant must justify in the application form why the publication is of sufficient impact to warrant support by the GPF.

Support from the GPF “will be given on a first come, first served basis” (see the news release). Will the GPF attract “up to 35 Open Access publications over the next 12 months“? If it does, then perhaps, as hoped by the OGI, “the launch of this fund will act as a catalyst for others to follow suit“.

More publication funds like the GPF would increase the pressure on publishers of high impact journals to provide OA options at prices that are acceptable to the agencies that sponsor such funds.

Although criticisms of the Journal Impact Factor (JIF) are well-known, it continues to be deeply embedded in the current academic culture. Perhaps, via publication funds like the GPF, the JIF can be utilized as a means to foster OA, rather than to inhibit it? Article-Level Metrics (ALMs) of the kind being developed by PLoS, also appear to have great potential as a means to foster OA.

However, publication funds designed to foster Gold OA should only be regarded as adjuncts to other approaches to the implementation of OA, not as replacements for them.

Comments (2)

What’s the future of OA?

Tom Wilson, in a message sent to the BOAI Forum on October 31, 2009, suggested that “… any strategy [for the OA movement] evolved today on the assumption that the future is likely to be the same as the past is probably going to fail“. Other excerpts:

No one knows exactly how the ‘open access’ movement will pan out ….. Strong advocacy of repositories is strong advocacy of the status quo in scholarly communication. ….. scholars are increasingly taking matters into their own hands and producing free OA journals on some kind of subsidy basis and any economist will tell you that social benefit is maximised by this form of OA.

Stevan Harnad, in a response to the same Forum, has reiterated some of his well-known perspectives:

The purpose of the Open Access movement is not to knock down the publishing industry. The purpose is to provide Open Access to refereed research articles. ….. The way to take matters in their [scholars’] own hands is to deposit the refereed final drafts of all their journal articles in their university’s OA Repository.

Comment: My own opinion is that both perspectives are tenable. I agree with Stevan Harnad that the most important short-term goal of the OA movement is to “provide Open Access to refereed research articles“. I also agree with Tom Wilson that ”No one knows exactly how the ‘open access’ movement will pan out” over the longer term, and that “the status quo in scholarly communication” seems likely to be unstable.

However, if the “status quo” is identified as a somewhat bewildering variety of options for scholarly communication that are changing quickly as technologies evolve, and are varying from field to field (and even across sub-disciplines in the same field), then this “status quo” may persist for quite a few years, before a smaller number of “best practices” become firmly established.

Leave a Comment

Addressing the scandal of the knowledge divide

An essay by Jean-Claude Guédon, Open Access and the divide between “mainstream” and “peripheral” science, was posted recently (July 23, 2009) at Mesa Redonda sobre Patrimonio Intelectual y Conocimiento Libre. [Apparently, this is a website supported by the Government of Venezuela – Google translation from Spanish to English: “Roundtable on Intellectual Heritage and Free Knowledge”]. A short excerpt from the latter part of this interesting essay:

This paper identifies the facets of the Gold and Green Roads that make sense in addressing the scandal of the knowledge divide. It brings to light essentially two fundamental strategies: on the Gold side, fully subsidized journals that do not financially penalize authors from poor countries, or do not submit them to humiliating forms of pleading for special treatment are essential. On the Green side of Open Access, the way to create symbolic value in competition with what presently supports the divide barriers is to organize a coherent system of institutional and thematic repositories. The former are charged with collecting and preserving all that they can and want to preserve. It is through institutional repositories that depositing mandates should be implemented as mandates can originate from a variety of institutions with some political clout, universities, research centres and granting agencies among them. However, it is through thematic repositories that the (research) wheat can be separated from the chaff and it is through them that various forms of new and useful forms of symbolic value can be created.

This essay had been deposited previously, as an eprint of a book chapter, in the E-LIS repository. The eprint was last modified on November 19, 2008. The citation indicates that this book chapter was expected to be “forthcoming in 2007, in Portuguese“.

Blog items (apparently, about an earlier version of the eprint) were posted by Peter Suber (OA for mainstreaming peripheral science) on December 1, 2007 and by Heather Morrison (National open access journal subsidy) on December 1, 2007. The eprint has been cited on CiteULike, and a version is also available via Scribd, posted on August 18, 2008 (see:

The version posted at the Venezuelan site has generated some recent interest on FriendFeed. See, for example, (July 25, by Bill Hooker) and (July 27, by Bora Zivkovic). Recommendation from Bora Zivkovic: “[Essay] by Jean-Claude Guédon is a Must Read of the day“.

Comment: An excerpt from Heather Morrison’s blog post is noteworthy:

Scielo is an excellent example of what can be accomplished through a nationally subsidized open access program. While the Scielo portal encompasses the scholarly work of many latin countries, Brazil alone, in 2005, brought 160 fully open access journals to the world at a very modest cost of only $1 million dollars.

Canada is experimenting with subsidized open access journals, through the Aid to Open Access Journals program.

Note: The link to the webpage for SSHRC’s Aid to Open Access Journals program has been updated in the excerpt. This  program has been renamed the SSHRC Aid to Scholarly Journals program. See also: About SSHC > Policy Focus > Open Access.

Leave a Comment

New OA Journal for single cell analysis

A new peer-reviewed OA journal, oap:single cell analysis, is intended “for papers pertaining to technology, application and research approaches for the biomolecular analysis of cells at a single cell level“.

On the Editorial Policy page, it’s  stated that authors retain copyright. On the Article Processing Charges page, the APCs for research articles and review articles are £499. There are no APCs for Editorials, Letters to the Editor, or Errata.

This is the first title to be produced by, a new site from Technology Networks Ltd. This online publisher also publishes several science portals, including

Leave a Comment

Update on OA journals from Academic Journals

On January 23 2009, there was a post, Many new and forthcoming OA journals from Academic Journals, by Gavin Baker, on Open Access News. A list of OA journals was included in the post, organized by launch date. Today, I visited the website of Academic Journals and reviewed their List of  Journals. At the end of the “Instructions for Authors” section of each journal, the current handling fee (article processing fee) for that journal can be found.

Below is a revised list of 54 journals, again organized by launch date.  For those journals with existing issues, the current handing fee has been added.

First online issue before 2009 (with date of first online issue):

* African Journal of Biotechnology (Nov 2002): $650
* Biotechnology and Molecular Biology Reviews (Apr 2006): $550
* Educational Research and Reviews (Apr 2006): $450
* African Journal of Agricultural Research (Aug 2006): $600
* International Journal of Physical Sciences (Sep 2006): $550
* International NGO Journal (Oct 2006): $300
* Scientific Research and Essays (Oct 2006): $550
* African Journal of Business Management (Feb 2007): $550
* African Journal of Microbiology Research (May 2007): $550
* African Journal of Political Science and International Relations (May 2007): $550
* African Journal of Biochemistry Research (June 2007): $550
* African Journal of Environmental Science and Technology (Aug 2007): $550
* Journal of Cell and Animal Biology (Aug 2007): $550
* Journal of  Medicinal Plants Research (Aug 2007): $600
* African Journal of Food Science (Sep 2007): $550
* African Journal of Plant Science (Sep 2007): $550
* African Journal of Pure and Applied Chemistry (Sep 2007): $550
* African Journal of Pharmacy and Pharmacology (Dec 2007): $600
* Journal of Geography and Regional Planing (Mar 2008): $550
* African Journal of Mathematics and Computer Science Research (Aug 2008): $550

First issue in January 2009:

* International Journal of Medicine and Medical Sciences: $750

First issue in March 2009:

* Journal of Plant Breeding and Crop Science: $550
* Journal of Psychology and Counseling: $550

Planned for March 2009:

* International Journal of Genetics and Molecular Biology
* Journal of Engineering and Technology Research
* Journal of Geology and Mining Research

Planned for April 2009:

* African Journal of History and Culture
* International Journal of Nursing and Midwifery
* International Journal of Vocational and Technical Education
* Journal of Accounting and Taxation
* Journal of Bacteriology Research
* Journal of Bioinformatics and Sequence Analysis
* Journal of Dentistry and Oral Hygiene
* Journal of Development and Agricultural Economics
* Journal of Ecology and The Natural Environment
* Journal of Economics and International Finance
* Journal of Educational Administration and Policy Studies
* Journal of Entomology and Nematology
* Journal of General and Molecular Virology
* Journal of Law and Conflict Resolution
* Philosophical Papers and Review

Planned for May 2009:

* African Journal of Marketing
* International Journal of Biodiversity and Conservation
* International Journal of Fisheries and Aquaculture
* International Journal of Library and Information Science
* International Journal of Livestock Production
* International Journal of Sociology and Anthropology
* Journal of Horticulture and Forestry
* Journal of Media and Communication Studies
* Journal of Parasitology and Vector Biology
* Journal of Pharmacognosy and Phytotherapy
* Journal of Public Administration and Policy Research
* Journal of Toxicology and Environmental Health Sciences
* Journal of Veterinary Medicine and Animal Health

[List modified on March 16 and 17, 2009]

Comments (1)

Harold Varmus interviewed

Dr Varmus, I presume? By David Worlock, Outsell’s Thinking Out Loud, October 15, 2008. Excerpts:

October 14 was the foundation date for PLoS Biology, as well as the designated Open Access Day, so the 300 STM publishers gathered at the STM Association’s annual meeting on that day at the Frankfurt Book Fair to hear this interview needed no reminder of the significance of Dr Varmus’ work. They may have been surprised, however, when he spoke as a publisher himself and shared some of his five years of experience.


The foundation of PLoS One as a fast track publication mode based on review of technical competence and eligibility, rather than scientific standing or originality, had been a great success, with a high proportion of submissions being accepted at a lower $1200 fee. The peer reviewed journals now had high reputations, and rejected some 90% of submissions, but had needed to raise fees beyond his forecast of five years ago to cover costs.


He is plainly interested by search tools and analysis, and while it remains his conviction that repositories like PubMed are a critical component, he wants to see the urge of scientists to cross search the literature on factors and issues of their own choosing as vital to eventual success, regardless of the conventional structures of current article publishing.


And in terms of new developments, he certainly sees the article as a work in progress, and was particularly strong on the need, where privacy and data regulation permitted, for more of the evidential base to be exposed to allow other scientists to examine the data from which conclusions had been drawn, and subject it to their own analytical techniques.

Recommendation: Read the entire text of the blog post from which these excerpts were taken.

Leave a Comment