Archive for June, 2009

Nature News Special on Science Journalism

Science Journalism, Nature Special 2009(June 24): “To mark the 6th World Conference of Science Journalists from 30 June-2 July 2009 in London, Nature is shining a spotlight on the profession in changing times. Science journalism faces an uncertain future. But to what extent should scientists help — or care?“.

Some of the articles indexed in this Special appear in the June 25 edition of Nature [2009; 459(7250)]. As is noted in a blog post by Maxine Clarke (Petrona, June 25, 2009), the three Essays and the Books&Arts article are free to read online for 2 weeks from the publication date.

The full text of News Feature by Geoff Brumfiel, Science journalism: Breaking the convention? (pages 1050-1) is also currently publicly accessible [PubMed Citation]. First paragraph:

Blogs and Twitter are opening up meetings to those not actually there. Does that mean too much access to science in the raw, asks Geoff Brumfiel.

Excerpts from the full text:

… During [conference] sessions, many group members posted brief comments sent from their laptops or mobile phones to the popular website Twitter, and automatically cross-posted to FriendFeed. …


For denizens of the blogosphere, these sorts of concerns [that these tools will undermine meetings] seem a little out of date. “I think scientific conferences are about your sharing with the world what you’re doing,” says Francis Ouellette, a researcher at the Ontario Institute for Cancer Research in Toronto, who twittered at the Cold Spring Harbor Meeting. “Whether or not the participant you’re sharing with is in the room is somewhat inconsequential.”

Ouellette and many other active bloggers are also members of the ‘open science’ movement, which encourages researchers to make their data public as quickly as possible. [Jean-Claude] Bradley sees this openness as a powerful deterrent to anyone hoping to scoop him at a conference because anything cribbed from his talk is already out on the Internet for everyone else to view. “If someone actually does copy something, I think it would be pretty embarrassing,” he says, “it’s already there, and it’s indexed to Google.”

This article by Geoff Brumfiel has generated a good deal of interest among users of tools such as FriendFeed. See, for example, results of a search of FriendFeed for the keywords: Science journalism: Breaking the convention?

The article has also been commented upon in the blogosphere. See, for example, Nature Takes A Look At Science Journalism, Lisa Green, NextBio Blog, June 30, 2009 [FriendFeed entry]. Excerpt:

… Some scientists worry about being scooped and dislike having the information they are willing to share verbally with conference attendees taken down as notes and made available on blogs or social networks. Other scientists see these digital communication tools as the way of the future and praise the increased efficiency of information sharing.

There has also been discussion of the Nature Science Journalism Special, initiated by Maxine Clarke on Nature Opinion forum. An example is her comment, posted on June 30. Excerpt:

… The open access point does not seem to me relevant as what journalists are interested in seeing is the paper before it is published, i.e. seeing an embargoed copy in advance of publication, not the business model that is used to publish it. …

The next comment is by Björn Brembs, also posted on June 30, 2009, on the same discussion thread, End of the line for science journalism? Excerpts:

Maxine: the problem is not access to that one single paper the press release cites. The problem is access to the papers the one under embargo should have cited but didn’t. ….. Without open access, any journalistic watch-dog must remain toothless – and toothless watch-dogs certainly won’t last long. …


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New OA Journal for single cell analysis

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

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

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

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CBCRA OA policy revised

An Open Access Policy was adopted by the Canadian Breast Cancer Research Alliance (CBCRA) in April 2007. This policy was revised in April 2009, and can be accessed via the CBCRA Open Access Archive subsection of the Research Program section of the CBCRA website. The CBCRA OA Policy has changed from a request to a requirement.

Revised Policy [PDF]. Excerpt:

CBCRA requires that grant holders supply an electronic copy of final, accepted manuscripts funded in whole or in part by CBCRA grants, to be posted in the CBCRA Open Access Archive, as soon as possible after publication. A publisher’s embargo period of up to six months will be permitted. The document must be either a publisher-generated PDF or the author’s final, accepted version, including changes introduced by the peer review process.

The first sentence of the previous policy was:

CBCRA requests that grant holders supply an electronic copy of final, accepted manuscripts funded in whole or in part by CBCRA grants.

Note that the word “requests” in this first sentence has been replaced by “requires” in the revised policy.

For a post by Peter Suber in Open Access News about the previous policy, see: CBCRA formally requests OA to the research it funds, October 2, 2007. (Coverage of CBCRA in Open Access News can be searched via:

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Literature search in ResearchGATE

ResearchGATE is “a free social networking site aimed at scientific researchers from all disciplines …” (excerpt from the current Wikipedia entry). I’ve recently become a member, but literature searches can be done by non-members. For example, a literature search for the key words “open access” AND “self-archiving” yielded 11 results. One for “open access self-archiving” yielded only 4 results. A search for “open access publishing” yielded 65 results.

Today, I initiated a thread on Open Access within the Science Communication Group.  (One needs to become a member to visit or contribute to this thread). The comment that I added is about a link to Peter Suber’sOpen Access Overview“, via:

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How to avoid questionable OA publications?

There has been much discussion recently about publishing ethics, initiated mainly by the “Bentham affair”. See, for example, Publishing ethics, open access, and OASPA;   OASPA launches a blog, comments on the Bentham affair;   Open-Access Publisher Appears to Have Accepted Fake Paper From Bogus Center;   Editors quit after fake paper flap (news item plus comments);   Fake journal, sham paper accepted. What other breaches of publication ethics have we yet to uncover?.

There was earlier discussion about the same publisher. For example: Black sheep among Open Access Journals and Publishers;   The Open Access Interviews: Matthew Honan;   More on Bentham.

So, how to know whether or not an OA publisher is “skeevy“? Dorothea Salo has posted some initial thoughts at: Opportunity in opprobrium, Caveat Lector, June 13, 2009. An OASPA certification program provides one way to approach the issue of quality regulation.

For individual authors considering the merits of an individual journal in the health sciences, PubMed can serve as a useful preliminary screening tool. Is the journal cited in PubMed? For example, the toll-access Bentham journal Current Cancer Drug Targets is included in PubMed, while the Bentham’s OA Open Cancer Journal isn’t.

The SCImago Journal & Country Rank (SJR) site can also provide useful information. For example, the SJR Journal Indicators for Cancer Research can be used to obtain a rank for Current Cancer Drug Targets. On June 14, it was 18th among Cancer Research journals, when ranked on the basis of SJR. In contrast, Open Cancer Journal can’t, at present, be found via a SJR Journal Search.

The site also includes data for Current Cancer Drug Targets, but, at present, no data for Open Cancer Journal.

Conclusion: Bentham’s Current Cancer Drug Targets is a much more reputable journal, at present, than its Open Cancer Journal.

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Steps a university can take in support of OA

See: Open Access at Concordia University: A Report for the Office of Research, Kathleen Shearer, March 27, 2009 [9-page PDF]. The report includes sections on: What is open access?; How is open access implemented?; State of play; Why does open access matter for Concordia?; Options.

The principal option that’s proposed is the implementation of an OA policy . It’s pointed out that a “sustainable OA repository is an essential element for supporting an open access policy“.

In addition to the adoption of an OA policy, it’s suggested that the university could join other universities in endorsing major open access statements, “to indicate to the international community [the university’s] formal commitment to open access.

Activities to support faculty members’ open access endeavors are also suggested. In particular, “the university might encourage faculty authors to modify restrictive publishing contracts so that they can deposit their work into an OA repository“.

The university “could also support the transition [of its university-based journals] to open access models by providing them with expertise and infrastructure support“.

Finally, “the university should continue the practice of giving due weight in promotion and tenure committees to peer-reviewed publications regardless of their price, medium, or business model, and also ensure that scholars are rewarded and encouraged for scholarly works whether or not they fall outside the traditional publishing system“.

The report also includes Annexes on: 1) Major Definitions of Open Access; 2) CIHR Policy on Access to Research Outputs September 2007; 3) Sample University Open Access Policies; 4) Further Reading.

Annex 3 includes the OA policies adopted by MIT Faculty and by the Harvard Faculty of Arts and Sciences.

Comment: This is a succinct and well-written report that was prepared for the Office of Research of Concordia University. However, it should be helpful to members of any university who are interested in supporting OA. For example, there’s an urgent need to ensure “that scholars are rewarded and encouraged for scholarly works whether or not they fall outside the traditional publishing system

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More on compliance with Wellcome Trust’s OA policy

In a blog post entitled “Journals compliant with Wellcome mandate” (UK PubMed Central Blog, June 1, 2009), Robert Kiley noted data indicating that (for Trust-funded research papers published between October of 2007 and August of 2008) potential compliance was about 95%, but actual compliance hovered around 35%. The data were taken from slide 14/21 of a presentation that’s available via another blog post, “Funder mandates” (UK PubMed Central Blog, May 29, 2009). The potential compliance estimate of 95% is based on the percentage of journals used by Wellcome-funded authors that have a “Wellcome compliant” publishing option. The Wellcome Trust’s OA policy is available at: “Position statement in support of open and unrestricted access to published research” (last updated February 2008).

An estimate of somewhat more recent compliance can be obtained via PubMed. As noted in a NLM Technical Bulletin from the National Library of Medicine, dated May 12, 2006, the search term “wellcome trust [gr]” can be used to retrieve citations (created since June 2, 2005) indicating Wellcome Trust support.

When this search was done (on June 8), but limited to articles published in the last 1 year, the proportion of articles for which the free full text was available was: 1527/4223 = 36%. When the same search was done for articles published in the last 180 days, the proportion with free full text was: 594/2088 = 28%. So, the proportion of articles with publicly-accessible full text, published between 6 months and one year ago, can be estimated to be: (1527 – 594)/(4223 – 2088) = 933/2135, or 43.7%.

Recent compliance with the Wellcome mandate appears to be approaching 44%. Might the difference between the earlier figure of about 35% and the estimate of close to 44% be explained by articles that are publicly accessible, but not via PMC/UKPMC? Examination of a sample of 100 articles published between 6 months and a year ago (and cited by PubMed) indicated that, for about 6% of these articles, the full text was publicly-accessible only via the journal site, not via PMC. (Usually, the full text was publicly-accessible via both PMC and the journal site).

If the estimate is correct that compliance with the Wellcome mandate (Trust-funded research articles must be available through PMC/UKPMC within 6 months after publication) appears to be about (44% – 6%) = 38%, then recent compliance is  close to the estimate of about 35% (see above), and still well below the estimated potential compliance figure of about 95%.

Added June 18, 2009: More extensive sampling has indicated that, for Trust-funded articles published between 6 months and a year ago (and cited by PubMed), the percentage for which the full text is publicly-accessible only via the journal site, and not via PMC, may be higher than 6%, and may be as high as 10%.

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