Archive for April, 2007

Open Medicine and the Platinum Route to OA

The new OA medical journal, Open Medicine, was launched earlier in this month, and has received some helpful publicity. See, for example, New medical journal to refuse drug industry advertisers,, April 24, 2007. An excerpt:

The editors note that by putting the onus on the end-user to cover publishing costs, knowledge is often not reaching professionals in poor countries, health care providers who don’t have access through a university, and patients who depend on the research.

Instead, they argue that the costs of publishing medical journals should be built into the grants that fund the research in the first place. “Without dissemination, knowledge cannot truly be said to exist,” they write.

In an item posted by Tom Wilson (Publisher/Editor in Chief, Information Research), on April 19, to the BOAI Forum, on the thread: Re: Independent open-access Canadian medical journal launches, Open Medicine is cited as another case study of the ‘Platinum Route’ to OA. The Platinum Route is “the voluntary, collaborative, no-charge model that is usually overlooked in the debates on OA“. He also provides links to other case studies of the Platinum Route, by Bo-Christer Björk, David J. Solomon and John Willinsky & Ranjini Mendis.

For those who have not yet had an opportunity to look at Open Medicine Vol 1, No 1 (2007), my own opinion is that the journal is off to a very good start. Some examples of its contents:

1) Why Open Medicine? By James Maskalyk, for the Editors of Open Medicine, pp. 1-2. Excerpt:

Information technology is evolving at a blistering pace. To try to keep step with its potential to influence medical science and practice, Open Medicine is hosting a blog on the topic. To manage it, we are using an open-source program (Drupal). So, too, for our manuscript management system (OJS).

2) A systematic review of studies comparing health outcomes in Canada and the United States, by Gordon H. Guyatt and co-authors, pp. 27-36. Excerpt:

Canadian health care has many well-publicized limitations. Nevertheless, it produces health benefits similar, or perhaps superior, to those of the US health system, but at a much lower cost. Canada’s single-payer system for physician and hospital care yields large administrative efficiencies in comparison with the American multi-payer model.

3) The joys and challenges of being an open-access medical journal, by Gavin Yamey (Magazine Editor, PLoS Medicine) and co-authors, pp. 46-48. Excerpt:

“In a world where political correctness obfuscates and public discussions are managed by public-relations firms and paid experts,” said John Hoey, former editor of the CMAJ, “there is a desperate need in medicine for open, plain-spoken discourse.”14

4) Pharmaceutical ethics?, a book review by Jerome P. Kassirer, pp. 58-59. Excerpt:

Eventually it becomes clear that the sole ethical issue addressed in this book is the disjunction between the profitability of drug companies and the vast health needs of the public; that is, between a profit-seeking corporate culture and societal responsibility.

5) The OM Blog (referred to in the editorial by James Maskalyk, see #1 above) already includes some items posted by the OM blogger, Dean Giustini of the UBC Biomedical Branch Library, Canada. An example is an item, Better outcomes in Canada, half the cost, about the systematic review by Gordon Guyatt and co-authors (see #2 above). The item has elicited some comments (mainly about search terms for the systematic review).


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Google Scholar and free versions of articles

A blog item was posted on March 1, 2007 about a puzzling differences between Google and Google Scholar (GS) in relation to access to a free version of articles. See: Google Scholar & free papers by Brett, Humber College, Toronto.

Excerpt: “Some more evidence of the weirdness is that GS doesn’t seem to know everything that just plain google knows. For example, if I copy the first line of the abstract and search for that in quotes, GS just shrugs its shoulders, while bare bones google serves up the required paper with its usual alacrity“.

Thanks to Matt Hodgkinson for the link to Brett’s blog item.

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A Wiki-based grantmaking strategy

An interesting OA-oriented strategic planning process has been initiated by The David and Lucile Packard Foundation. It has set up a Wiki Site for Nitrogen Strategy Development.


Our Conservation and Science Program currently awards grants totaling approximately $45 million annually in the areas of coastal conservation, fisheries conservation, climate change, and science. If the Board decides to add an additional nitrogen/agriculture focus, the scale of investment in the new area is likely to be on the order of $5 million to $15 million per year.

A decision to establish a grantmaking program on nitrogen/agriculture will depend on whether the Foundation has developed a compelling grantmaking strategy, which details the goals, outcomes, strategies, and activities that it will pursue. It includes information that characterizes the risk associated with the approach (i.e., how likely is it that the grant investment will achieve the desired outcomes) and the time frame for the investment. The strategy seeks to address the question, What is the most effective way to spend the funds available in order to help solve this problem? …

Foundations regularly use grantmaking strategies to orient their philanthropic investments. These strategies are typically developed by foundation staff, by philanthropic intermediaries, or by consulting firms. Through this Wiki site, we would like to experiment with an alternative to these models for strategy development. We are concerned that the existing models for strategy development cast far too narrow a net in their search for creative solutions. They are unable to benefit from the wisdom, experience, and expertise present within civil society, private sector, and academic institutions. …

Through this Web site,, the Packard Foundation would like to bring the wisdom of crowds to bear on the development of a possible grantmaking strategy. Our hope is that this will help to improve the goals and elements of any such strategy, while also helping the Foundation to identify individuals, institutions, and projects that could play a role in carrying it out. If successful, we also believe that the Wiki site could help to inform the work of other organizations and the grantmaking strategies of other foundations. …

Excerpts from the Frequently Asked Questions:

What does the Packard Foundation plan to do with the information it collects through this process?

Packard will use the ideas and information generated by the online discussions and wiki to inform its strategy for funding the most effective approaches to reducing nitrogen pollution. In addition, the Foundation strongly encourages participants of to make use of the ideas generated by this community in their own work.

How long will be accessible?

The online discussions and wiki will be live from March 30-April 30, 2007. After that, the product of the community’s work will remain available to the public, archived online and protected under a Creative Commons License.

How will Packard share lessons learned?

Packard will be writing an account of what happened and what was learned from This account will be posted on both the archived site and, and sent to all participants in the collaboration.

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Collecting public information from diverse sources

A very interesting article by Gary Bader, entitled Open Access and Open Source Speed Computational Network Biology Research, was posted on 9 April 2007 at the University of Toronto’s Project Open Source|Open Access website. Excerpts:

A major challenge for studying the cellular network is collecting all known public information from very diverse sources, such as the biomedical literature, raw experimental data and the hundreds of existing pathway databases. Open access content and open source software systems are critical for overcoming this challenge. Once information is freely shared in open, standard formats, it can be aggregated, integrated, searched, visualized and analyzed.

Pathway Commons will be a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.

As one example of why such a database might be accessed, consider the OA article e-published on 22 March 2007 by Bowie MB, Kent DG, Dykstra B, McKnight KD, McCaffrey L, Hoodless PA, Eaves CJ, Identification of a new intrinsically timed developmental checkpoint that reprograms key hematopoietic stem cell properties, Proc Natl Acad Sci USA. 2007(Apr 3);104(14):5878-82. An excerpt:

Preliminary analysis of the molecular mechanism(s) involved (18) indicates that it affects a pathway affected by c-kit, a key receptor in mouse HSC self-renewal control and one whose activation differentially regulates fetal and adult HSC self-renewal both in vivo and in vitro (12, 28).

Entry of c-kit into the Search Pathway Commons box at the Pathway Commons site yields Pathway: Signaling events mediated by Stem cell factor receptor (c-Kit).

Pathguide currently contains information about 224 biological pathway resources. Many are freely available.

These examples illustrate the urgent need for agencies that support research to put into place policies of the kind being developed by the Canadian Institutes of Health Research (CIHR), on Access to Research Outputs.

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