Archive for May, 2010

Selected OA news items noted during May 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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Selected OA news items noted during April 2010

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