Posts Tagged scholarly publishing

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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Finding influential OATP news items

The Open Access Tracking Project (OATP) provides a unique resource. It distributes information about recent news items of interest from the perspective of the Open Access movement. Participants in the OATP tag new developments using Connotea. The OATP links include project feeds that contain all (and only) the items that participants have tagged with One of the feeds is a Twitter feed, based on the version of the Connotea RSS feed showing the 50 most recent items.

Some influential news items are bookmarked in Connotea by more than one participant. One of the useful OATP mashups is a filtered version of the project feed, a “OATP 100 items no dups” feed of the 100 most recent news items, without duplicates.

Influential news items are also often found in multiple tweets, or have been retweeted, via Twitter. Another useful resource is Topsy, a “search engine powered by tweets“. Topsy provides way to assess the influence of news items that have been included in the OATP Twitter feed. One can simply use Topsy’s Advanced Search option to search within the Twitter user OATP. Such searches within the OATP Twitter feed can be restricted to the current day, or week, or month. The number of duplicate tweets (or retweets) about a news item can be used as a quantitative indicator of the influence of a particular news item. (It’s the URL of the news item that counts, not the exact text of the tweet). This indicator provides one kind of “article-level metric” (ALM) for that news item. (For an informative commentary about ALMs, see the OA article: Article-Level Metrics and the Evolution of Scientific Impact by Cameron Neylon and Shirley Wu, PLoS Biol 2009(Nov); 7(11): e1000242. [PubMed citation]).

An example of a very influential news item (well over 900 tweets, including the one from the OATP) during the week ending on July 24, 2010 was: BP buys up Gulf scientists for legal defense, roiling academic community | (See all of the Twitter trackbacks for this news item, via Topsy). The Connotea bookmark for this news item was tagged oa.industry,, oa.negative, by Peter Suber (Connotea user “petersuber“).


Efforts to keep up with recent news items involve three major aspects. Firstly, there must be ways for the news items to be discovered. Secondly, ways are needed to filter the discovered items so that those of particular interest to an individual user can be identified easily. Thirdly, the discovered items of interest must be accessible to the reader.

About discovery: The Open Access movement may be unique, from a scholarly perspective, in the extent to which credible items of interest are distributed across the entire Web. A wide variety of online sources provide relevant items. The participants in the OATP (especially, Peter Suber) have been extraordinarily diligent in their efforts to discover such items. Additional news items can be identified via these tags: #openaccess and #oa. There is much overlap between these latter results, because both of these hashtags are often used together. I’ve not yet found an easy way to assess the extent of overlap between news items identified by the #openaccess or #oa hashtags and those included in the OATP feeds. There’s a feed that combines the OATP results with those for #openaccess, but duplicates between the two have not been eliminated.

About filtering: The tags added to Connotea bookmarks can be used to filter news items obtained via the Connotea site. An example is provided by the results of a search for oa.canada. Unfortunately, the Connotea search engine tends to function slowly, especially when combinations of tags are sought.  Searches via Topsy are more convenient, but Topsy does not recognize “” or “oa.canada” as hashtags, in the absence of a “#” symbol. My own experience so far has been that, thanks to the OATP, there’s less of a discovery deficit when seeking OA-related news items, and more of a filtration challenge. What are the most efficient ways to find those news items of greatest personal interest? They may not always be items that have a noteworthy number of Twitter trackbacks.

About access: there’s an advantage to the fact that credible news items of interest to the OA movement are widely distributed across the entire Web. Unlike articles in traditional toll-access academic journals, OA-related news items tend (not a surprise) to be publicly accessible, usually via Gratis OA. Perhaps the OA movement is in the process of providing an initial test of the conjecture that we are in the early stages of a growing movement to abandon traditional academic publishing? Or, perhaps more realistically, in the early stages of a growing movement to supplement traditional academic publishing with a variety of other approaches, all based on free and open services?

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UC versus NPG: First Round

UC threatens ‘systemwide boycott’ of Nature Publishing Group – June 09, 2010 by Daniel Cressey, The Great Beyond (a Nature blog), June 9, 2010. Excerpts:

The University of California is mulling a boycott of Nature Publishing Group in response to what it claims is a proposed 400% increase in subscription fees to the group’s journals, a letter from the university’s libraries reveals.


Nature News has asked NPG for a response to the letter. It will be posted here as soon as we have it.

The letter is: Re: Informational Update on a Possible UC Systemwide Boycott of the Nature Publishing Group, California Digital Library, University of California, June 4, 2010.

More about the letter:

U. of California Tries Just Saying No to Rising Journal Costs by Jennifer Howard, Chronicle of Higher Education, June 8, 2010.

California throws the gauntlet in NPG’s face by Dorothea Salo, The Book of Trogool, June 8, 2010.

Possible Boycott of Nature Publishing Group Journals: an Open Letter from Gary Strong, University Librarian, to UCLA Faculty by Gary E Strong, Louise M Darling Biomedical Library Blog, June 8, 2010.

Some relevant FriendFeed entries, dated: [June 8][June 8[[June 9][June 9].

Comment: This is just Round One of what should be a very interesting fight negotiation. What will be the response by NPG to the letter from UC?

Added June 10, 2010: A response from NPG: Public statement from Nature Publishing Group regarding subscription renewals at California Digital Library (CDL), June 9, 2010. Found via: California libraries gearing up for fight against Nature (Updated) by John Timmer, Ars Technica, June 9, 2010.

Added June 12, 2010: Response to the public statement from NPG: Response from the University of California to the Public statement from Nature Publishing Group regarding subscription renewals at the California Digital Library, June 10, 2010. Found via: Nature Publishing Group Defends Its Price Increase for U. of California by Jennifer Howard, The Chronicle of Higher Education, June 9, 2010.

See also: Librarians at the gate over licensing rate by Paul Jump, Times Higher Education, June 11, 2010.

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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.

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Survey by Project SOAP

An email was received from BioMed Central today about Project SOAP. The message:

Your views on Open Access publishing are needed!

Dear Colleague,

BioMed Central has partnered with CERN, The Max Planck Society, and others in the European Commission-funded project SOAP – a Study of Open Access Publishing.

The project analyzes researchers’ attitudes towards, knowledge of and experiences with open access. The resulting insights as well as recommendations will be shared with the European Commission, publishers, research funding agencies, libraries and researchers.

Your contribution will be very valuable in shaping the public discourse on open access and we would be very grateful if you could take 10-15 minutes to complete this survey.

Please follow this link:

Thank you in advance for your help,

BioMed Central

It happens that I had already completed the survey. It did require only about 10-15 minutes to complete. I found Question 23 especially interesting:

23. Listed below are a series of statements, both positive and negative, concerning Open Access publishing. Please indicate how strongly you agree/disagree with each statement.

[Responses are via a 5-level Likert item in typical format: ‘Strongly agree’; ‘Agree’; ‘Neither agree nor disagree’; ‘Disagree’; or ‘Strongly disagree’].

Open Access publishing leads to an increase in the publication of poor quality research

[That OA scientific journals won’t preserve the quality/pedigree of science is one of the  suggestions made by Eric Dezenhall to the Association of American Publishers – see Open Access to Science Under Attack by David Biello, Scientific American, January 26, 2007. For a recent response  to a suggestion of this kind, see: PLoS ONE: Editors, contents and goals, available via:]

Open Access unfairly penalises research-intensive institutions with large publication output by making them pay high costs for publication

[This is an issue for Gold OA based on article-processing fees (APFs) – see, for example,  Science in the open, Nature Materials 2009; 8: 611. For some comments about this issue, see: More on the costs of scholarly communications, Peter Suber, May 22, 2008]

It is not beneficial for the general public to have access to published scientific and medical articles

[From a health-sciences perspective, this is a version of what BioMed Central has identified as (Mis)Leading Open Access Myth 4]

Publicly-funded research should be made available to be read and used without access barrier

[For a detailed analysis, see: The taxpayer argument for open access by Peter Suber, SPARC Open Access Newsletter, September 4, 2003]

Open Access publishing is more cost-effective than subscription-based publishing and so will benefit public investment in research

[For a summary of a pro-OA perspective on this issue, see: Major new report on the economic implications of OA, Peter Suber, Open Access News, January 27, 2009]

Articles that are available by Open Access are likely to be read and cited more often than those not Open Access

[This is actually two questions. The ‘read more?’ issue is currently less controversial than the ‘cited more?’ issue. For an extensive bibliography from The Open Citation Project, see: The effect of open access and downloads (‘hits’) on citation impact: a bibliography of studies]

If authors pay publication fees to make their articles Open Access, there will be less money available for research

[For a pro-OA response, see what BioMed Central has identified as (Mis)Leading Open Access Myth 1]

Researchers should retain the rights to their published work and allow it to be used by others

[See, for example: Retain copyright, in the Open Access section of the website of the University of Ottawa]

Open Access publishing undermines the system of peer review

[Another suggestion made by Eric Dezenhall was to “Paint a picture of what the world would look like without peer-reviewed articles” (quoted in Open Access to Science Under Attack by David Biello, Scientific American, January 26, 2007). See also:  Will open access undermine peer review?, Peter Suber, SPARC Open Access Newsletter, September 2, 2007]

Comment: A weakness of the SOAP Survey is that it appears to be feasible to respond to it more than once.

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Ten Years of PubMed Central

The blog post PubMed Central Turns Ten – Dr. David Lipman, by Dean Giustini (Open Medicine Blog, April 21, 2010), includes a link to
a video (51 min), entitled “Ten Years of PubMed Central “.

It’s a video of a talk given by David Lipman, Director of the National Center for Biotechnology Information at the National Library of Medicine, on March 23, 2010. He provides an overview of the past, present, and future of the National Institutes of Health’s archive of biomedical research articles, PubMed Central (PMC). Some noteworthy sections of the video are:

0 – 3:30 min: Introduction by Ian Lapp, Mailman School of Public Health (which cosponsored the event).

3:30 – 22:40 min: David Lipman describes the past of PMC.

22:40 – 31:30 min: He discusses the “Discovery Initiative”, an effort to “improve the quantity, quality and relevance of information obtained/viewed by users“. The value of weblog analyses is emphasized.

31:30 – 32:25 min: PMC statistics (as  of January 2010) are discussed.

32:25 – 38:50 min: Changes in written communication are considered.  Some very interesting comments are made about use of the Google knol authoring system to produce a new kind of journal, PLoS Currents: Influenza. Plans to produce other journals using this same authoring system are mentioned. These plans include additional PLoS Currents journals, but also journals initiated by other groups.

39:20 – 51 min: Discussion. The initial question is about the process for starting a Google knol journal.

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Can the costs of quality-filtration be reduced?

The costs of the conventional ‘hierarchy of journals’ approach to the quality-filtration of the research and scholarly literature can be very high.

For example, Mike Rossner, Executive Director of the Rockefeller University Press, has quoted a figure of US$10,000 as the average cost per article for the online versions of the three journals that this press publishes. These journals (and their 2008 Journal Impact Factors) are: J Cell Biol (9.1), J Exp Med (15.5) and J Gen Physiol (4.7). He provided this cost figure at the 07:50 min. point during his presentation at an event held on March 9, 2010 by the Scholarly Communication Program at Columbia University.

The full 97 min. video of the presentations is available at: Who Pays for Open Access?. Mike Rossner is the first of three speakers. He called these Rockefeller University Press journals ‘selective journals’, and described their business model, which provides free public access to articles after a 6-month embargo period. He suggested (at the 18:25 min. point in the video) that, for biomedical research journals, “charging for information in only the first 6 months after publication is a clear-cut way to know how valuable it is“.

The costs per article for these ‘selective journals’ are high mainly because of staffing costs of the ‘publication platform’. Tasks such as the management of the peer review system and the performance of copy-editing are done by paid staff. These people must deal with all of the manuscripts that are received, even though only about 10% of them are published.

Mike Rossner also suggested (at the 14:00 min. point in the video) that PLoS ONE provides an example of his definition of an ‘archival journal’ – one where: “Reviewers ask if data support conclusions, not whether the research represents an advance in the field “. An ‘archival journal’ publishes a higher proportion of submitted articles than does a ‘selective journal’. This higher volume reduces costs.

The current publication fee for PLoS ONE is US$1,350. This figure probably overstates the actual cost per article, if PLoS is indeed using PLoS ONE to subsidize its more selective journals (see the 14 min. point in the video, and, for example, Bulk Publishing Keeps PLoS Afloat, Philip Davis, The Scholarly Kitchen, July 7, 2008).

In contrast, Green OA costs much less. To date, an exemplar for Green OA is the arXiv repository, which provides OA to e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. The cost of per submission for an article in the arXiv repository is much, much lower than the publication fee for PLos ONE. It’s less than US$7 per article (see the section on “How much does arXiv cost to operate? ” in the arXiv Support FAQ).

This much lower cost was mentioned (at the 48:35 min. point in the video) by Ivy Anderson, Director of Collection Development and Management at the California Digital Library, the second speaker in the event at Columbia University (whose presentation begins at the 18:50 min. point in the video). However, she also pointed out that arXiv is primarily a repository. It’s not a publishing platform.

Although submission to the arXiv doesn’t involve peer review, there is an arXiv moderation system. Excerpt:

The arXiv moderators are experts in their fields and in the types of submissions that are appropriate for their subject classifications. They evaluate based on the content of the submission and the policies of arXiv.

In an analogous way, the OA collection PLoS Currents: Influenza also uses a Board of Expert Moderators. In the PLoS Currents FAQs, it’s stated (here) that:

There are currently no publication charges for PLoS Currents. However, it is possible that we will introduce a small publication charge in future to cover the running costs.

It’s also stated, near the bottom of the same FAQs page, that: “We intend PLoS Currents: Influenza to be the prototype for additional PLoS Currents sites“.

Comments: The entire video (Who Pays For Open Access?) is recommended, including the presentation by the third speaker (Bettina Goerner, Manager, Open Access for Springer, beginning at 51:40 min. in the video) and the discussion session (beginning at 72:25 min.).

So, how best to increase the cost-effectiveness of quality-filtration of the research and scholarly literature? One can ask (as does Mike Rossner at the 17:40 min. point in the video): “Has the revolution in searchability negated the utility of selective journals as filters of information?“. He thinks that it hasn’t (and won’t for some time).

Perhaps, if PLoS Currents: Influenza is successful, in that it’s valued by it’s users and it’s running costs are low, then this peer moderation-based approach to quality-filtration of contributions to specified areas of research may flourish, as it has for those specified areas served by the arXiv.

It’s noteworthy that some basic article-level metrics (ALMs) are also provided for each contribution to PLoS Currents: Influenza. These include statistics about “Views” and “Comments“, together with “Ratings“. One need not wait for citation data in order to obtain some guidance about those contributions to this collection that are already attracting attention.

For more about the need for sophisticated ALMs, see: Article-Level Metrics and the Evolution of Scientific Impact by Cameron Neylon and Shirley Wu, PLoS Biol 2009(Nov); 7(11): e1000242. See also the “Metrics” and “Comments” that are attached to this same article.

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Video on importance of OA for research from Kenya

Prof. Mary Abukutsa-Onyango discusses the importance of Open Access for research from Kenya and other African countries, Leslie Chan, Bioline News Blog, March 27, 2009. Video (08:45 min) posted March 27, 2010 on Vimeo and March 20, 2010 on YouTube. See also [FriendFeed entry].

About this video:

In an interview conducted by Leslie Chan of Bioline International, Prof. Mary Abukutsa-Onyango of Jomo Kenyatta University of Agriculture and Technology discussed the challenges she faced when trying to publish her original research on African Indigenous Vegetables (AIV) in “international” journals, and the importance of Open Access journals in Africa in ensuring that important research relevant to the continent are being published, read, and applied. The implications of Open Access for development in African countries were also discussed. The interview was recorded on Feb. 19th, 2010 at the University of Nairobi during a Workshop on Increasing the Impact of Research through Open Access, co-hosted by the University of Nairobi Library, eIFL.Net and Bioline International.

For an example of an article by Mary Abukutsa-Onyango in the African Journal of Food, Agriculture, Nutrition and Development (AJFAND), see: The role of home gardening in household food security in Butere division of Western Kenya, Musotsi, AA; Sigot, AJ & Onyango, MOA, AJFAND 2008; 8(4): 375-90. Abstract:

Gardening remains the most important method of food production for a majority of people in the developing world, yet high population density has put a lot of pressure on land as more of it is required for settlement. This has led to land fragmentation, which has negatively affected food production, hence, resulted in food insecurity. Food insecurity is a concern today in many parts of Kenya. Land use practices thus have to be intensified to maximize food production on the small land available. Home gardening has been identified as a means of providing all year round access to food for rural households. Home gardens can make a significant contribution in meeting daily household needs for better nutrition and health. A study was carried out among rural households in Butere division, western Kenya, to determine the role of home gardening on household food security. Simple random sampling was used to obtain a study population of 100 households, to whom an interview schedule and an observation checklist was administered. Twenty key informants were purposively sampled and responded to questionnaires. Data obtained were analyzed quantitatively. Pearson correlation coefficient was applied on home gardening indicators: size of land for home gardening, home garden crops and home garden livestock, and food security indicators: food stock and number of meals eaten daily by households. Results obtained showed that home gardening plays a significant role in food security of rural households with respect to size of land and food stock (0.336 at p≤0.01), and number of livestock and food stock (0.211 at p≤0.05). Home gardening did not play a significant role in food security with regard to home garden crops. Households, therefore, should be empowered and encouraged to improve their practice of home gardening to realize food security. Findings of this study will be useful to governmental and non-governmental bodies involved in promoting food security in the rural households.

See also the Bioline International entry for AJFND and the home page for AJFND Online.

Comment: One of Prof. Abukutsa-Onyango’s noteworthy comments about “the challenges she faced when trying to publish her original research on African Indigenous Vegetables (AIV) in ‘international’ journals” was that the AIVs were dismissed by some people as ‘weeds’. See the article KENYA: No longer a weed, IRIN Africa, August 7, 2009.

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Acceptance of technological changes

If Open Access to electronic versions of the peer reviewed literature is regarded as a technological change (or, an ‘invention’, in comparison with toll access), then what factors might be expected to influence the acceptance of such ‘inventions’ within a society? On the basis of his examination of the literature on technological change, Jared Diamond identified four main factors. (See Chapter 13 of “Guns, Germs and Steel: The Fates of Human Societies“, W W Norton, 2005 edition).

The four factors: 1) Relative economic advantage compared with existing technology; 2) Social value and prestige (which can override economic benefit, or lack thereof); 3) Compatibility with vested interests; 4) Ease with which the advantages of the invention can be observed.

The primary producers of the peer reviewed literature (researchers and scholars) may differ in their perspectives, about a least some of these factors, from the perspectives of the institutions that support their work (such as universities, research institutes and funding agencies).

From the perspective of individual researchers and scholars, there’s no obvious economic advantage to themselves that can be attributed to OA. For example, any extra time (or funds) required to achieve Green (or Gold) OA could instead be devoted to research or scholarship.

If OA yields economic advantages, they are likely to be achieved at levels beyond that of the individual researcher, e.g. by leading to a much more efficient and effective system for the dissemination of research outputs. The institutions that support individual investigators are much more likely to be concerned about such economic advantages than are individual researchers or scholars.

From the perspective of individual researchers and scholars, social value and prestige are linked to the indicators currently used (e.g. by promotions committees at universities and research institutes) to assess research or scholarly productivity. The journal Impact Factor (IF) continues to be the main quantitative indicator that’s used for this purpose (in spite of it’s well-known defects when used to assess the productivity of individuals, and especially, when used to compare the research outputs of individuals who have contributed to different research areas). Long-established, high-IF traditional toll-access journals have an advantage over more recently-initiated Gold OA journals. The Green Route to OA (via OA repositories) is permitted by many of these high-IF traditional toll-access journals. However, compromises must often be accepted, such as an embargo period between the date of publication and the date of OA, and/or access only to the final post-peer review postprint, rather than to the ‘version of record’.

Compatibility with vested interests is obviously an important factor. As noted above, the use of quantitative indicators (especially IFs) to assess research or scholarly productivity is deeply embedded into the policies and procedures of promotions committees at universities and research institutes, and into those of peer review committees at funding agencies.  As a consequence, whatever their personal views about how best to assess research productivity, individuals supported by these institutions must take this vested interest in such indicators into account when they consider routes of publication.

Of course, the publishers of traditional toll-access journals have an even stronger vested interest in maintaining (as much as possible) a system that they have dominated, and from which they’ve benefited, both economically and socially.

Finally, again from the perspective of individual researchers and scholars, the advantages of OA may not be easy to observe. The extent to which OA provides a citation advantage continues to be controversial, and probably varies across different research areas. The likelihood that OA increases and broadens attention to research outputs is less controversial. However, appropriate indicators (such as ‘Article-Level Metrics’, designed to provide credible multidimensional quantitative measures of the impact of individual publications) are still at an early stage of development.

Institutions that support research and scholarship may be more interested in the uses that are made of the new knowledge produced by the individuals that they have supported than are those individuals themselves. This question is asked: Has this new knowledge led to useful practical applications, of the kind that may serve to provide evidence that the public investment in the supporting institutions has yielded identifiable social or economic benefits?

If these four factors are indeed applicable to the acceptance of OA, then it’s not surprising that OA hasn’t yet become the dominant route to the quality-filtered research and scholarly literature.

How best to foster changes in the ways in which these four factors influence the acceptance of OA? So far, institutions that provide support for research (and especially, funding agencies) appear to be playing leadership roles in fostering appropriate changes. Acceptance of OA does appear to be increasing, although slowly.

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Guidance re data sharing and patient privacy

New guidance on data sharing will minimize risks to patient privacy, EurekAlert, January 28, 2010.

And: BMJ policy on data sharing, Trish Groves, BMJ 2010(Jan 28); 340: c564 (Editorial; only the first 150 words are publicly accessible).

See also: How to publish raw clinical data: guidelines from Trials and the BMJ, Matthew Cockerill, BioMed Central Blog, January 29, 2010.

About this article: Preparing raw clinical data for publication: guidance for journal editors, authors, and peer reviewers by Iain Hrynaszkiewicz, Melissa L Norton, Andrew J Vickers, Douglas G Altman, Trials 2010(Jan 29); 11(1): 9 [Epub ahead of print][Connotea bookmark][PubMedCitation].

This article has been co-published: BMJ 2010(Jan 28); 340: c181 [PubMed Citation]. Summary points:

Despite journal and funder policies requiring data sharing, there has been little practical guidance on how data should be shared

Confidentiality and anonymity are key considerations when publishing or sharing data relating to individuals, and this article provides practical advice on data sharing while minimising risks to patient privacy

Consent for publication of appropriately anonymised raw data should ideally be sought from participants in clinical research

Direct identifiers such as patients’ names should be removed from datasets; datasets that contain three or more indirect identifiers, such as age or sex, should be reviewed by an independent researcher or ethics committee before being submitted for publication

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