Posts Tagged OA publishing

How to select an Open Access journal?

Introduction

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.

Publishers

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.

Comment

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

The Selected Journals

#1) BMC Medicine: http://www.biomedcentral.com/bmcmed
Scope: Original research, commentaries and reviews that are either of significant interest to all areas of medicine and clinical practice, or provide key translational or clinical advances in a specific field.
Journal Impact Factor (JIF): 6.035
Article Processing Fee (APF): £1515/€1785/US$2325. See:  http://www.biomedcentral.com/bmcmed/about/apcfaq/howmuch
Licence: Creative Commons CC-BY (must attribute the work).
Article-Level Metrics: Via Altmetric.com (see: “About this article” under the “Associated Material” in the right-hand column that’s shown for each published article). An example: http://www.biomedcentral.com/1741-7015/11/124/about
Peer Review: Reviewers are named and reviewers’ reports are published. An example: http://www.biomedcentral.com/1741-7015/11/3/prepub

#2) BMC Medical Genetics: http://www.biomedcentral.com/bmcmedgenet
Scope: Considers articles on the effects of genetic variation in individuals, families and among populations in relation to human health and disease.
JIF: 2.33
APF: £1290/€1520/US$1980. See: Article Processing Charge FAQ #3.
Licence: CC-BY
Article-level metrics: Via Altmetric.com (see “About this article”, as described above for BMC Medicine).
Peer Review: Reviewers are named and reviewers’ reports are published. An example: http://www.biomedcentral.com/1741-7015/11/106/prepub

#3) BMJ Open: http://bmjopen.bmj.com/
Scope: Publishes medical research from all disciplines and therapeutic areas.
JIF: Currently being tracked for its first JIF. [Announced June 20, 2013: First JIF is 1.58].
APF: £1350. See: http://bmjopen.bmj.com/site/about/faqs.xhtml#11
Licence: The default licence is CC-BY-NC (Attribution-NonCommercial), but where the funder requires it the author can select CC-BY. See: Compliance with Funders Open Access policies.
Article-level metrics: Article Usage Statistics are provided. An example: http://bmjopen.bmj.com/articleusage?rid=3/3/e002114
Peer Review: Reviewers are named and reviewers’ comments are published. An example is available [PDF].

#4) eLife: http://elife.elifesciences.org/
Scope: From basic biological research through to applied, translational and clinical studies.
JIF: No JIF yet. New journal, launched in 2012.
APF: Free of charge, at least for an initial period. Supported by the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust.
Licence: CC-BY
Article-level metrics: Number of views, PDF downloads and XML downloads are provided for each article.
Peer Review: The decision letter from the editor and the author response are published, if author agrees. An example: http://elife.elifesciences.org/content/2/e00499 (look under “Jump to” in the right-hand column).

#5) PeerJ: https://peerj.com/
Scope: Research Articles in the biological and medical sciences.
JIF: No JIF yet. New journal, launched in 2013.
APF: No APF. Uses membership plans instead.
Licence: CC-BY
Article-level metrics: Via ImpactStory.
Peer Review: Reviewers may be anonymous but reviewers’ comments are published, if author agrees. An example: https://peerj.com/reviews/68/

#6) Biology Direct: http://www.biology-direct.com/
Scope: Genomics, Bioinformatics and Systems Biology; Immunology; Mathematical Biology.
JIF: 4.02
APF: £1290/ €1520/US$1980. See: Article-processing charges FAQ #3.
Licence: CC-BY
Article-level metrics: Via Altmetric.com.
Peer Review: Reviewers are named and reviewers’ reports are published. A commentary about open review in Biology Direct is available here. An example: http://www.biology-direct.com/content/8/1/3#sec5

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

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

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

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

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

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

#13) F1000Research: http://f1000research.com/
Scope: All articles, including research findings, analyses of scientific developments, opinions, and comments are published immediately, following a quick internal check for obvious inappropriateness.
JIF: No JIF yet. New journal, launched in 2012.
APF: US$1000 for research articles. See: Article Processing Charges.
Licence: CC-BY
Article-level metrics: Number of views, PDF downloads and XML downloads are provided for each article.
Peer Review is post-publication. Reviewers are named and short reviewer reports are published. Articles that pass post-publication peer review will be indexed by PubMed. At present, this indexing hasn’t begun yet. See some critical comments here.

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

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

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Comments (5)

Questions about uptake of Springer’s hybrid OA option

A news release, Springer Open Choice uptake affects 2011 journal pricing (EurekAlert, June 18, 2010), raised questions about uptake of the Springer Open Choice option, a hybrid OA option.  Searches of PMC (PubMed Central) can provide some relevant information. Examples:

Q#1: Was uptake of Springer Open Choice greater in 2009 than in 2008?

A: Yes. When “Limit by Journal” was used to restrict the search of PMC to “Springer Open Choice” (“Journal Name”), then the number of articles published in the date range “2009/01/01” to “2009/12/31” was found to be (Search #1): 2186. For the date range “2008/01/01” to “2008/12/31”, the result was (Search #2): 1079. So, these results indicate that the uptake of the Springer Open Choice option did increase substantially between 2008 and 2009.

Q#2: Does the Springer Open Choice option account for a substantial proportion of the OA publications available via PMC?

A: No. The proportion of the PMC Open Access Subset identified as being associated with the Springer Open Choice option was found (on June 21, 2010) to be 2186/40196=5.4% in 2009. This is an increase in this proportion in comparison with the previous year. The results for 2008 were:  1079/31006=3.5%.

Q#3: How does uptake of the Springer Open Choice option compare with that of other hybrid OA options?

A: Quite well. Data were obtained, using searches analogous to those considered above, for the percentages of “Elsevier Sponsored Documents” (PMC’s nomenclature) in the PMC Open Access Subset (1.1% in both 2009 and 2008) and for the percentages of “Wiley-Blackwell Online Open” (PMC’s nomenclature) publications in the PMC Open Access Subset (1.0% in 2009 and 1.6% in 2008).

Of course, many other publishers provide hybrid OA options. For a list, see: Publishers with Paid Options for Open Access (via SHERPA/RoMEO, University of Nottingham).  The hybrid OA options of only a few of the major publishers on this list could be identified among PMC’s “Journal Names”. These included (in order of decreasing uptake into PMC): “BMJ Unlocked“, “ACS AuthorChoice“, “Taylor & Francis iOpenAccess” and “SAGE Open“. The uptake into PMC of the latter four hybrid OA options was less than that found for the Springer, Elsevier and Wiley-Blackwell hybrid OA options.

Data for the Oxford Open hybrid OA option could not be obtained via searches of PMC. However, a recent press release, Open Access Uptake for OUP Journals: Five years on (Oxford Journals News, June 10, 2010) , included the information that: “On a like-for-like basis, the average uptake in 2009 for journals which entered the scheme prior to 2008 was stable (6.7%, compared with 6.8% in 2008).” (These percentages represent the average uptake of the Oxford Open option for papers in participating OUP journals, taking into account a lower uptake amongst 11 new titles joining Oxford Open in 2009. They should not be compared with the percentages of hybrid OA publications in the PMC Open Access Subset).

Q #4: How does uptake of the Springer Open Choice option compare with data for PLoS ONE?

A: Better than anticipated. Data were obtained, using searches analogous to those considered above, for the percentages of publications in the PMC Open Access Subset that were published in PLoS ONE. The results, 11.0% in 2009 and 8.7% in 2008, are only approximately twice as large as the results for the Springer Open Choice option (5.4% in 2009 and 3.5% in 2008, see Q#2 above).  PLoS ONE was selected for this comparison because it’s a broad based (and very high volume) fully OA journal that seems likely to grow even larger in the future (see Comments, below).

Comments:

Data have been obtained, via PMC, about the uptake of the hybrid OA options of several major publishers. The Springer Open Choice option appears to have had the greatest uptake in 2008 and 2009. Perhaps this is because Springer was one of the earliest adopters of a hybrid OA option, which it launched in 2004 (see: Springer’s Open Choice program, Peter Suber, Open Access News, July 3, 2004). Springer has also actively marketed this option, via deals such these, also reported in Open Access News: Max Planck and Springer strike a deal (February 4, 2008) and Springer’s first US deal in which subscriptions cover publication fees for affiliated authors (January 21, 2009).

Of course, like it or not, one of the major marketing tools for journals is their Journal Impact Factor (JIF). Fully OA journals can have an JIF, but the hybrid OA components of otherwise toll-access journals currently do not.

Thomson Reuters recently released its 2009 Journal Citation Report. An excerpt from: New impact factors yield surprises (The Scientist, June 21, 2010):

PLoS ONE debuted in the Journal Citation Report for the first time with a respectable impact factor of 4.351. This score puts the open access journal in the top 25th percentile for biology publications. But might this sudden success be more of a bane than a boon to PLoS ONE, blogger Philip Davis asks. It may turn out that accepting 70 percent of the manuscripts submitted to your journal gets a bit trickier when you’re flooded with papers.

Thus, a surprisingly large initial JIF for PLoS ONE provides support for the prediction that this OA journal will grow even larger in the future. Will such growth pose problems of scalability for PLoS ONE? Perhaps – but these will be problems arising from success. Nice problems to have. Much better than the most unattractive alternative, which is failure.

Can the hybrid OA options offered by toll-access journals also increase their uptake? Perhaps, if these options are actively marketed, and can compete successfully in prestige and price with fully OA journals. Springer also has a nice problem. It now owns BioMed Central (BMC) a pioneering OA publisher. See: Springer acquisition FAQ. An excerpt from the FAQ:

7. Will BioMed Central’s article processing charges be raised to match those of the Springer Open Choice option?

No, BioMed Central will continue to set its own article processing charges, and no increases are planned as a results of the acquisition. As ever, BioMed Central reserves the right to adjust article processing charges from time to time in the light of economic factors.

So, Springer’s Open Choice option is competing with Springer’s own fully OA publisher. Might both of Springer’s approaches to Gold OA fail to compete successfully with those of other publishers? Seems unlikely.

Comments (3)

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“.

Comments:

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)

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:
http://www.surveymonkey.com/s/soap_survey_c

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: http://ff.im/jPasa]

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.

Comments (4)

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.

Comments (1)

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. www.bioline.org.br

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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