Posts Tagged open science

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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Policy change before peer review: OA needed?

A noteworthy situation has been reported in several recent articles. Public health policy (in this case, about flu shots) is being influenced by a research study that is currently undergoing peer review at an unidentified medical journal.This situation provides an attention-grabbing example of the dilemma in research ethics that must be faced about  preliminary research results of great public interest. Should such results be available for public scrutiny as soon as possible? Or, should concerns about impact on public perceptions (or, misperceptions) justify delays while experts in the field evaluate the results?

One solution to this dilemma has been the recent launch of PLoS Currents: Influenza: “PLoS Currents: Influenza aims to enable this exchange [of scientific results and ideas] by providing an open-access online resource for immediate, open communication and discussion of new scientific data, analyses, and ideas in the field of influenza. All content is moderated by an expert group of influenza researchers, but in the interest of timeliness, does not undergo in-depth peer review“.

Comment: My own preference? The tradeoff between possible risks and possible benefits is a challenging one, but I favor the use of PLoS Currents: Influenza as the less paternalistic route. [See Wikipedia entries about paternalism and soft paternalism]. [See also a previous post in this blog about PLoS Currents].

Examples of relevant articles about this situation:

1) MOH cautious on flu shot fears by Helen Branswell in, September 23, 2009 [Twitter entry][FriendFeed entry]. Excerpt:

Unpublished Canadian data are raising concerns about whether it’s a good idea to get a seasonal flu shot this season.

2) Like several other provinces, BC, PEI, to delay seasonal flu shots for under 65s by Helen Branswell, Canadian Press, September 28, 2009 [Twitter entry][FriendFeed entry]. Excerpt:

British Columbia and Prince Edward Island have joined a growing list of provinces that have announced they will delay part of their seasonal flu shot programs this year, decisions which are partially fuelled by concerns raised by controversial and unpublished Canadian research.

3) More flu programs suspended by Caroline Alphonso, The Globe and Mail, September 29, 2009. Excerpts:

Lead authors, Danuta Skowronski of the British Columbia Centre for Disease Control and Gaston De Serres of Laval University, have submitted their findings to an unnamed scientific journal and may not comment until it is published.


The findings have yet to be published, but word of it has prompted provinces and territories to revamp their vaccination programs.

4) B.C. announces seasonal and H1N1 flu vaccine strategy by Shane Bigham, News1130, September 28, 2009. Excerpt:

The postponement of the seasonal flu shot is also in response to an unpublished Canadian medical study which seems to indicate that people who have received the seasonal flu shot are more likely to catch the H1N1. The findings of that study are still up for peer review and have not been reported in other parts of the world.

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How to create an open scientific culture?

Doing science in the open, Michael Nielsen,, May 1, 2009. Excerpts:

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals and not in more modern media.


To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: first, build superb online tools; and second, cause the cultural changes necessary for those tools to be accepted. The necessity of accomplishing both these tasks is obvious, yet projects in online science often focus mostly on building tools, with cultural change an afterthought. This is a mistake, for the tools are only part of the overall picture. It took just a few years for the first scientific journals (a tool) to be developed, but many decades of cultural change before journal publication was accepted as the gold standard for judging scientific contributions.

None of this is to discount the challenge of building superb online tools. To develop such tools requires a rare combination of strong design and technical skills, and a deep understanding of how science works. The difficulty is compounded because the people who best understand how science works are scientists themselves, yet building such tools is not something scientists are typically encouraged or well suited to do. Scientific institutions reward scientists for making discoveries within the existing system of discovery; there is little space for people working to change that system. A technologically challenged head of department is unlikely to look kindly on a scientist who suggests that instead of writing papers they would like to spend their research time developing general-purpose tools to improve how science is done.

What about the second task, achieving cultural change? As any revolutionary can attest, that is a tall order. Let me describe two strategies that have been successful in the past, and that offer a template for future success. The first is a top-down strategy that has been successfully used by the open-access (OA) movement. The goal of the OA movement is to make scientific research freely available online to everyone in the world. It is an inspiring goal, and the OA movement has achieved some amazing successes. Perhaps most notably, in April 2008 the US National Institutes of Health (NIH) mandated that every paper written with the support of their grants must eventually be made open access. The NIH is the world’s largest grant agency; this decision is the scientific equivalent of successfully storming the Bastille.

The second strategy is bottom-up. It is for the people building the new online tools to also develop and boldly evangelize ways of measuring the contributions made with the tools. To understand what this means, imagine you are a scientist sitting on a committee that is deciding whether or not to hire a scientist. Their curriculum vitae reports that they have helped build an open-science wiki, and also that they write a blog. Unfortunately, the committee has no easy way of understanding the significance of these contributions, since as yet there are no broadly accepted metrics for assessing such contributions. The natural consequence is that such contributions are typically undervalued.

To make the challenge concrete, ask yourself what it would take for a description of the contribution made through blogging to be reported by a scientist on their curriculum vitae. How could you measure the different sorts of contributions a scientist can make on a blog — outreach, education and research? These are not easy questions to answer. Yet they must be answered before scientific blogging is accepted as a valuable professional scientific contribution.

Recommendation: Read the entire text of this excellent post. [Found via: The Tree of Life, Jonathan A Eisen, May 9, 2009].

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On the commons (and MaRS)

MaRS (a not-for-profit corporation founded in 2000 and located in Toronto’s downtown “Discovery District”) hosts a blog. A recent post in the ‘Today’s Picks‘ category of the blog is Valuing the commons, by Kathryn Fitzgerald, 24 July 2007. An excerpt:

The idea of a commons encompassing both tangible natural resources and intangible assets like information is gaining ground in contemporary discourse. The concept has been used to support diverse goals, from the regulation of carbon dioxide to open access to information. In business, the idea of the commons drives the corporate social responsibility movement, and is the inspiration behind entrepreneur Peter Barnes’ recent book, Capitalism 3.0: A Guide to Reclaiming the Commons.

Also, links are provided to:

Creative Commons


Science Commons

What’s MaRS about? As noted in the webpage Explore MaRS,

MaRS is a convergence innovation centre dedicated to accelerating the commercialization of new ideas and new technologies by fostering the coming together of capital, science and business.

So, MaRS can be regarded as a Canadian example of a contemporary approach to science policy. (See also some comments about science policy in the previous post, Open Access Science and Science Policy).

For more information about MaRS, see:

MaRS Discovery District (via the website of the Office of the Premier of Ontario)

Visit MaRS (via the website of the Innovations Group, University of Toronto)

MaRS Phase 2 (John Barber. Globe & Mail, 19 June 2007, via the Forum)

MaRS Discovery District (from Wikipedia)

One of the MaRS Centre tenants is the Ontario Institute for Cancer Research (OICR). On 30 May 2007, I attended an event at the MaRS Center (I’m grateful to the OICR for the invitation). This is a news item about the event: Canada and California team up in fight against cancer. Might this latter collaboration involve, as it develops, some “open access science”? I hope so.

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The Future of Science is Open

Bill Hooker has posted a series of three very interesting articles, on: I) Open Access; II) Open Science; and, III) An Open Science World. Here, I’ll pay particular attention to the first article of the series, on Open Access, and especially to the list of benefits of Open Access. I’ve included some selected excerpts from the text, just to highlight some of the points that are made.

I) The Future of Science is Open, Part 1: Open Access. 3 Quarks Daily, Bill Hooker, 30 Oct. 2006.

Benefits of Open Access:

1. Maximal research efficiency. Excerpt: “The usual version of Linus’ Law says that given enough eyeballs, all bugs are shallow — meaning that with enough people co-operating on a development process, nearly every problem will be rapidly discovered and solved. The same is clearly true of complex research problems. and OA provides a powerful framework for co-operation.”

2. Maximal return on public investment. Excerpt: “Why should taxpayers pay twice, once to support the research and then again when the scientists they are funding need access to the literature? More importantly, open access to a body of knowledge makes that knowledge more available and useful to researchers, physicians, manufacturers, inventors and others who make of it the various socially desirable outcomes, such as advances in health care, that government funding of research is intended to produce.”

3. Advantages for authors. Excerpt: “There is a large and steadily growing body of evidence showing that OA measurably increases citation indices (that is, the number of times other papers refer to a given article).”

4. Advantages for publishers. Excerpt: “the benefits that accrue to authors of OA works also work to the advantage of publishers: more widely read, used and cited articles translates to more submissions and a wider audience for advertising, paid editorials and other value-add schemes.”

5. Advantages for administrators. Excerpt: “Open access, by removing the subscription barriers that splinter the research literature into inaccessible proprietary islands, raises the possibility of vast improvements in our ability to measure and manage scientific productivity.”

6. Scalability. Excerpt: “For end users to keep pace with the explosive growth of available information, the cost of access has to be kept down to the cost of getting online.”

II) The Future of Science is Open, Part 2: Open Science. 3 Quarks Daily, Bill Hooker, 27 Nov. 2006.

For what I am calling Open Science to work, there are (I think) at least two further requirements: open standards, and open licensing.”

III) The Future of Science is Open, Part 3: An Open Science World. 3 Quarks Daily, Bill Hooker, 22 Jan. 2007.

Here I want to move from ideas to applications, and take a look at what kinds of Open Science are already happening and where such efforts might lead. Open Science is very much in its infancy at the moment; we don’t know precisely what its maturity will look like, but we have good reason to think we’ll like it.”

I urge anyone who is interested in Open Access and Open Science to read each of these articles.

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