Guidance re data sharing and patient privacy

February 7, 2010 at 5:24 pm · Filed under Open Access ·Tagged , , , ,

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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Updates sent to Twitter, January 2010

January 31, 2010 at 11:21 pm · Filed under Open Access ·Tagged ,

Updates related to OA, sent to Twitter during January 2010:

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More about UKPMC

January 21, 2010 at 1:12 am · Filed under Open Access

UKPubMedCentral – an Open Access digital library of biomedical science by Douglas Kell, Professor Douglas Kell’s blog, January 18, 2010. Excerpt:

To address the linked problems of accessing and then exploiting the biomedical literature, a variety of scientific funders in the UK have in the first place, and over time, been developing the wherewithal to make as many abstracts and full papers as possible available to all (“Open Access”), by mirroring a similar initiative led from the USA as PubMedCentral. The second problem is necessarily addressed by appropriate computer software that ‘reads’ all of the papers and develops methods of ranking and presenting appropriate analyses, and here the UK version has now developed some important innovations, based not least on the methods of text mining.

Comment: As noted in the FAQ “How does UK PubMed Central differ from PubMed and PubMed Central?“: “Unlike PubMed Central, UKPMC provides a single point of access to not only full-text articles but additionally the abstracts available through PubMed. The UKPMC interface offers different features and functionality. The UKPMC service has been designed and built in close consultation with researchers within the UK.“

The features of the beta version of UKPMC are summarized at: “About UK PubMed Central“. For example, UK PubMed Central Plus (UKPMC+) can be used by researchers who have a grant awarded by any of the UKPMC funders to:

* view Web of Science and Scopus citation counts for their publications
* report on the outcomes of their grants
* link publications to grants
* submit their manuscripts

It can be anticipated that PMC Canada will, as it’s developed further, provide features and functionality of value to researchers within Canada, and especially (at least initially) to researchers supported by the Canadian Institutes of Health Research (CIHR), one of the partners involved in the development of PMC Canada.

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Preliminary data about CIHR-supported publications cited in PubMed

January 8, 2010 at 1:29 am · Filed under Open Access ·Tagged , , ,

Technical Bulletin No. 372 of the U.S. National Library of Medicine (NLM) was posted on January 5, 2010. Excerpt:

Effective mid-October 2009, when a published article has an acknowledgement of funding support from the Canadian Institutes of Health Research (CIHR), that information is added to the PubMed journal citation.

At present, a search using the country name alone (a search on ‘canada [gr]‘) retrieves the relevant records, because CIHR is the only Canadian organization in the Grant Number field in PubMed at this time.

Thus, it’s now feasible to obtain, via PubMed, data that will provide  indicators of compliance with the Policy on Access to Research Outputs of the CIHR. This policy “applies to all grants awarded January 1, 2008 and onward, which have received funding in whole or in part from CIHR“.

For example, the Advanced Search option in PubMed can be used to obtain an estimate of the total number of CIHR-supported publications with a publication date in the last 2 months of 2009. The result (search #1): 867.

Of these, links to ‘free full text’ were available for a total of (search#2): 82 (9.5% of 867). Of these 82 publications, 23 (28%) were published in PLoS ONE (search#3).

Analogous data can be obtained for several topics (such as ‘Cancer’). Total number of cancer-related (and CIHR-supported) publications with a publication date in the last 2 months of 2009 (search #4):  221. Number of these for which links to ‘free full text’ were available (search #5): 23 (10% of 221). Of these 23 publications, 7 (30%) were published in PLoS ONE (search #6). (The other 16 articles were distributed across 14 different journals).

Comment: As the Policy on Access to Research Outputs of the CIHR is implemented, one can expect to see an increase in the percentage of CIHR-supported publications (cited in PubMed) for which links to ‘free full text’ will be available. As noted in NLM Technical Bulletin No. 372:

A PubMed Central Canada manuscript submission system will be implemented in early 2010. This will be another source for grant information from the Canadian Institutes of Health Research.

(Note: the link to PMC Canada in the current version of NLM Technical Bulletin No. 372 is corrupted).

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Updates sent to Twitter, December 2009

December 31, 2009 at 12:35 pm · Filed under Open Access ·Tagged ,

Updates related to OA, sent to Twitter during December 2009:

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Contribution to the OSTP Policy Forum

December 20, 2009 at 7:29 pm · Filed under Open Access ·Tagged , ,

Today (December 20) is the last day for contributions to the first phase of the Public Access Forum, sponsored by the White House Office of Science and Technology Policy (OSTP): Policy Forum on Public Access to Federally Funded Research: Implementation.

The next phase, to begin on Dec. 21, is described at: Public Access Policy Phase One Wrap-Up: Implementation. Phase Two of this forum will focus on “Features and Technology”. It’s scheduled to run from Dec. 21 to Dec. 31. Phase Three, focused on “Management”, is expected to run from Jan. 1 to Jan. 7. (Initially, this Policy Forum was scheduled to end on Jan. 7, but the timeline has been extended by two weeks. The current plan is to “use those last two weeks to revisit, on a more detailed level, all three focus areas that will have been addressed by then“).

My own contribution to the first phase, posted today, was:

Thanks for the opportunity to post a comment. OSTP has provided innovative leadership in it’s initiation of this Policy Forum.

Who should enact public access policies?:
• Agencies that fund a significant amount of research should enact mandatory policies. Some differences in policies across agencies may be necessary at this time, but researchers (and their institutions) should not be overburdened by too many differing implementation requirements.

Version and Timing:
• The author’s final version, after peer review, of papers stemming from all publicly-funded research should be required to be deposited into an open, central repository immediately upon acceptance for publication. The author(s) should retain copyright to this version.

Mandatory:
• Deposit should be mandatory, by funders and also by each sponsoring institution. Persistent failure by authors to comply with such a policy should lead to appropriate penalties (such as ineligibility for further funding).
• Deposit should be in a central repository. There are already two successful central repositories, arXiv and PMC. (What’s missing is a successful one for all of the social sciences and humanities). Harvesting from the central repository into the sponsoring institution’s repository should be feasible, if desired by the sponsoring institution (to reduce the burden on researchers and their sponsoring institutions).

Other:
• From an international perspective, there should be harmonization of policies by those agencies in different countries that support similar kinds of research. For example, the requirements for deposition in PMC, UKPMC and PMC Canada should not differ.
• The value-added services offered by these repositories could differ. For example, an ideal value-added service would be the provision, for each article in a repository, of credible article-level metrics (ALMs). The Public Library of Science (PLoS) has already done pioneering developmental work on such ALMs (http://www.plos.org/cms/node/485). The repositories of sponsoring institutions could also provide value-added services not already available via the central repositories.

Comment: These comments are, of course, my own. They do not represent the views of any of the institutions or organizations with which I’m associated.

The only aspect of my comments that’s at all novel is probably the suggestion that deposition in both central repositories and the repositories of sponsoring institutions would permit each type of repository to offer different value-added services to authors and users. My current view is that such value-added services are needed to establish (or enhance) differences in “brand” across different repositories, and to increase the appeal of repositories to authors and users.

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Policies of OA journal funds about hybrid OA

December 14, 2009 at 12:55 am · Filed under Open Access ·Tagged ,

The Open Access Directory page about OA journal funds provides a list of university funds to support OA journals. Policies about the use of these funds vary across universities. For example, some university funds will pay publication fees of hybrid journals, while others will not.

Funds that currently state clearly that they will not pay publication fees of hybrid journals include those of Cornell, ETH Zurich, Harvard, Lund U and U of Oregon.

Funds that currently will pay publication fees of hybrid journals, but have a cap on the maximum to be paid, include those of U of California at Berkeley (capped at $1500 per article, 4 awards per fiscal year per author), U of North Carolina-Chapel Hill (capped at $1000 per article) and the U of Wisconsin-Madison (30% of fee, to a maximum of $1500 per article, one award per fiscal year per author).

The fund of the U of Calgary currently will pay publication fees only of hybrid journals “that reduce subscription fees in response to the take-up of their Open Access programs“.

The fund of the U of Ottawa currently will pay publication fees of hybrid journals only if the journals “make articles available immediately or allow open access self-archiving immediately upon publication (no embargo period imposed)“.

The current policy about the fund of the U of Nottingham simply states that the OA fees charged by hybrid journals “can be covered by the use of the University Open Access Publishing Fund“, and provides an email address to which enquiries to access the Fund should be directed.

Comment: A major concern is that some publishers of hybrid journals indulge in “double dipping” – taking money to make articles OA without reducing their subscription fees. See, for example, Open access: are publishers ‘double dipping’? by Daniel Cressey, The Great Beyond (a Nature blog), October 20, 2009.

This is the main reason why several OA journal funds will not pay publication fees of hybrid journals, and why the fund of the U of Calgary tries to avoid support for double-dipping. However, how to be sure that double-dipping isn’t happening?

Some of the complexities involved in hybrid journal pricing have been considered in two posts (post I and post II) by Bernd-Christoph Kämper to the Lis-e-resources mailing list on October 20, 2009. His warning (also applicable to attempts to ensure that double-dipping isn’t happening): “Don’t cheer too soon” .

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More about PMC Canada

December 4, 2009 at 12:14 am · Filed under Open Access ·Tagged , , ,

The webpage entitled: Update on PubMed Central Canada (PMC Canada), at the Canadian Institutes of Health Research (CIHR) website, was modified on November 30, 2009. Excerpt:

The first element of the PMC Canada system-the search interface-was launched in October 2009. It allows users to browse, search and download articles.
A manuscript submission system is being developed for PMC Canada.

Also, there’s a section on “PMC Canada: Now Open for Business” by Andrea Szwajcer in the November 2009 issue [5-page PDF] of a newsletter from the St. Boniface Hospital Library (one of the University of Manitoba Libraries). An excerpt (from page 3 of the newsletter):

The digital platform to locate and access publications includes a basic and advanced search function for PMC Canada as well as alphabetical index list to search the PMC Journals by title. The manuscript submission system is not yet available but is promised “later this year”.
This webpage is a little deceiving as you may assume that if you do a search in the search box, you are limited to strictly Canadian publications or have that ability somehow. The reality is a little more disappointing. ….

Comment: Relevant information is available via the webpage for PMC International (PMCI). Excerpts:

To date, NLM has authorized two PMCI centers: UKPMC and PMC Canada.

…..

Like the UKPMC, PMC Canada receives all of its content through the US PubMed Central.

…..

With the introduction of PMC Canada, all current PMC participants have been asked for permission to make their PMC content available to the Canadian site. NLM will not redistribute a journal’s PMC content to PMC Canada without the explicit permission of the publisher. These permissions are included automatically in PMC agreements signed in June 2009 forwards.

So, all articles in PMC Canada that are marked “In PMC Canada” will also be available in US PMC. Those marked “Only in US PMC” aren’t currently available in PMC Canada because the publisher has not yet provided explicit permission for them also to be archived there.

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Updates sent to Twitter, November 2009

November 30, 2009 at 11:47 pm · Filed under Open Access ·Tagged ,

Updates related to OA, sent to Twitter during November 2009:

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arXiv repository to be enhanced

November 24, 2009 at 1:22 pm · Filed under Open Access ·Tagged , ,

Stimulus grant to enhance arXiv e-preprints for scientists by Bill Steele, Chronicle Online, Cornell University, November 17, 2009. Excerpts:

Soon, Cornell’s e-print arXiv of scientific papers will evolve from a simple database to a place where “authors, articles, databases and readers talk to each other” to help users identify a work’s main concepts, see research reports in context and easily find related work.

…..

Other enhancements will provide interoperability with such research sites as PubMedCentral and provisions to allow scientists to contribute in newer, more flexible text formats.

Researchers might be more enthusiastic about participating in open access journals and repositories if they could see that their work was more accessible and usable, [Paul] Ginsparg suggested. “And perhaps the academic community will again play a role at the forefront as the semantic Web 3.0 rolls out,” he said. Academic publishing has lagged behind the commercial Internet in providing interactive enhancements that today’s students take for granted, he explained. “Configuring research communications infrastructure for the next generation of researchers requires getting into the heads of near-term future researchers — undergrads and grad students — coming of age in the Google/Facebook/Twitter era.”

Found via posts in [Digital & Scholarly] and [Open Access News].

Comment: The arXiv repository has been at the forefront of the Green route to OA. The proposed enhancements may once again permit it to play a leadership role. These enhancements are intended to add value of a kind that will enhance the appeal of repositories to a wider range of users.

Green OA mandates implemented by funding agencies and universities can be regarded as “sticks”, designed to push appropriate content into repositories. Enhancements of the kind being proposed for the arXiv can be regarded as “carrots”, designed to pull a variety of users toward repositories. The latter approach has, so far, received less attention from OA advocates than the former.

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