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Lee Dirks

We are profoundly saddened by the untimely and tragic death of our dear friend and colleague Lee Dirks, who was killed together with his wife Judy Lew in a road accident in the Peruvian Andes.

Lee had recently been elected to the Board of Directors for Dryad.  He also served on the Board of Visitors for the UNC School of Information Sciences (of which he was a proud alumnus) and was a member of the Board of the SILS Metadata Research Center.  Lee made a named for himself in recent years as Director of Education and Scholarly Communication at Microsoft.

Lee was a visionary information scientist, a warm and generous personality, and a man who loved adventure.  The number of people whose lives he touched in his own short life was staggeringly large.

Lee and his wife are survived by their two young daughters, who were at home in Seattle at the time of the accident.  Our thoughts are with them.  And we will miss Lee greatly.

Our guest post today is from Mohamed Noor of Duke University, president of the American Genetic Association. The AGA is a scholarly society dating back to 1903.  AGA, together with Oxford University Press, publishes the Journal of Heredity, which is a charter member in the Dryad organization and one of the first journals to integrate manuscript and data submission with the repository.  The society just held their annual symposium in Durham, North Carolina, not so far from Dryad’s NESCent headquarters, and has some excellent news to report from the Council meeting.

The American Genetic Association is pleased to announce that it has now fully adopted the Joint Data Archiving Policy (JDAP) for the Journal of Heredity.  The Journal of Heredity had previously required that newly reported nucleotide or amino acid sequences, and structural coordinates, be submitted to appropriate public databases. For other forms of data, the Journal “endorsed the principles of the Joint Data Archiving Policy (JDAP) in encouraging all authors to archive primary datasets in an appropriate public archive, such as Dryad, TreeBASE, or the Knowledge Network for Biocomplexity.”

This voluntary archiving policy was facilitated by the direct link between the Journal of Heredity and Dryad, in effect since February 2010.

To further support data-sharing and data access, in July 2012, the AGA Council voted unanimously to make data archiving a requirement for publication, under the terms specified in the JDAP.

The requirement will take effect by January 1, 2013. The American Genetic Association also recognizes the vast investment of individual researchers in generating and curating large datasets. Consequently, we recommend that this investment be respected in secondary analyses or meta-analyses in a gracious collaborative spirit.

Many other leading journals in ecology and evolutionary biology have adopted policies modeled on JDAP over the past two years, and other journals are invited to consider it as a policy that has attracted wide support among scientists.

Dryad is delighted to join with PLOS today to announce our partnership with PLOS Biologyas described here on the official PLOS Biology blog, Biologue.  As the first Public Library of Science (PLOS) journal to partner with Dryad to integrate manuscript submission, “PLOS Biology can offer authors a seamless tying together of an article with its underlying data; [and] can also provide confidential access for editors and reviewers to data associated with articles under review.”
PLoS Biology - www.plosbiology.org

Here’s how it works: During manuscript evaluation, PLOS Biology invites authors to deposit the underlying data files in Dryad, sending them a link to Dryad which enables a streamlined upload process (no need to enter the article details).  Authors may deposit complex and varied data types in multiple formats, and these files are then accessible to editors and reviewers by anonymous and secure access during the manuscript review process.  Behind the scenes, the journal’s editorial system and the Dryad repository exchange metadata, ensuring that upon publication, the article links to the associated data in Dryad, and permanently connecting the published article with its securely archived, publicly available data.

Dr. Theodora Bloom, Chief Editor, PLOS Biology, mentions that journals “are uniquely well-placed to help researchers ensure that all data underlying a study are made available alongside any published articles.”

We welcome PLOS Biology authors and editors to Dryad, and look forward to extending this partnership to other PLOS journals.

Are you a librarian wondering what Dryad can do for you, and you can do for Dryad?  Please see our guest post on “Dryad for the Science Librarian” over at the New England eScience Portal.

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We are happy to have the opportunity to reproduce here, with permission, the full text of the recent editorial by Trish Groves and Fiona Godlee in BMJ entitled “Open Science and Reproducible Research” [BMJ 2012; 344:e4383], which also announces an expanded partnership between Dryad and BMJ, a leading publisher of biomedical research journals.

New reports call for scientists to share data and publishers to embrace open access

by Trish Groves, deputy editor, BMJ, and Fiona Godlee, editor in chief, BMJ. Published 26 June 2012

“Scientists should communicate the data they collect and the models they create, to allow free and open access, and in ways that are intelligible, assessable and usable for other specialists . . . Where data justify it, scientists should make them available in an appropriate data repository.” [1]

So said the Royal Society last week, in its report Science as an Open Enterprise: Open Data for Open Science. The report calls for more openness among scientists and with the public and media; greater recognition of the value of data gathering, analysis, and communication; common standards for sharing information to make it widely usable; mandatory publishing of data in a reusable form to support findings; more expertise in managing and supporting the use of digital data; and new software tools to analyse data. It is time for a big shift, says the report, from the status quo where “many scientists still pursue their research through the measured and predictable steps in which they communicate their thinking within relatively closed groups of colleagues; publish their findings, usually in peer reviewed journals; file their data and then move on.”

A few days earlier the UK government’s working group on expanding access to published research findings, chaired by Janet Finch, recommended a “clear policy direction to support publication in open access or hybrid journals, funded by article processing charges, as the main vehicle for the publication of research, especially when it is publicly funded.” [2, 3]  The Finch report urges funders to establish more effective and flexible arrangements to meet the costs of publishing in open access and hybrid journals; publishers to minimise restrictions on the rights of use and reuse of text and other content, especially for non-commercial purposes; funds to be found to extend and rationalise licences and subscription arrangements for research generated in the United Kingdom and published in pay walled journals; and repositories to be developed to complement formal publishing. But the report warns that the transition to widespread open access publishing will take time and money, and meanwhile the effects of the transition on subscription based journals (which still provide the bulk of peer review and set standards for high quality publishing) must be carefully considered to minimise damage to the learned societies and publishers that run them.

As Finch explains in a podcast interview with BMJ editor Fiona Godlee, access to published articles and access to data are separate matters, but both can potentially benefit the public. Indeed, major funders—including the Wellcome Trust, US National Institutes of Health, and UK Medical Research Council—have jointly stated their belief that “making research datasets available to investigators beyond the original research team in a timely and responsible manner, subject to appropriate safeguards, will generate three key benefits: faster progress in improving health, better value for money, and higher quality science.” [4]

These funders do not yet, however, mandate data sharing. They should. The ability of doctors to make the right decisions with patients about the benefits, harms, and costs of treatments and tests depends increasingly on high quality learning and guidance, which, in turn, depend on a robust evidence base that is as complete and as transparent as possible. We cannot rely only on results in published research articles and trial registries because they are often incompletely and selectively reported [5].  Moreover, drug regulators often lack access to full data reported in confidence, let alone to publicly accessible data [6].

Data sharing can greatly increase dissemination, meta-analysis, and understanding of research results; it can also aid confirmation or refutation of research through replication [7],  allow better implementation of research findings [8], and increase transparency about the quality and integrity of research. It does bear some technical challenges and risks: these include potential invasion of participants’ privacy and breaking of patients’ confidentiality, inappropriate data manipulation, compromised academic or commercial primacy, and breach of intellectual property rights and journal copyright, but none of these should be insurmountable [9].

So let’s get on with it. Since 2009 the BMJ has asked authors to state at the end of their article whether they will allow their data to be accessed or even reanalysed by others [10]. Many authors have agreed to share their anonymised data. To make it easy for authors to do this, the BMJ is partnering with the Dryad online repository (http://datadryad.org/), something that our sister journal BMJ Open has been doing for some time. Fifteen datasets from BMJ Open articles are already posted, as well as one from the BMJ [11].

Meanwhile, we are stepping up the BMJ’s commitment to open access. After the success of last year’s pilot, we have introduced article processing fees for all published research articles. Fee waivers and discounts are available for authors who are unable to pay, and editors will be unaware of whether a fee has been paid when making their decision on publication.

With these latest high level UK reports, and the growing support of research funders around the world [4], the move towards open access has reached a tipping point. The BMJ was the first major general medical journal to make research articles freely available online and has maintained its commitment to open access ever since. We will continue to debate, test, implement, and promote new ways to support authors in the publication of their work, and to achieve worldwide access to research results and data.

References

  1. Royal Society. Science as an open enterprise: open data for open science. 2012. http://royalsociety.org/uploadedFiles/Royal_Society_Content/policy/projects/sape/2012-06-20-SAOE.pdf
  2. Working Group on Expanding Access to Published Research Findings: the Finch group. 2012. Accessibility, sustainability, excellence: how to expand access to research publications. www.researchinfonet.org/wp-content/uploads/2012/06/Finch-Group-report-FINAL-VERSION.pdf
  3. Hawkes N. Open access to research findings will deliver huge benefits but will not be cost free, report says. BMJ 2012; 344:e4248.
  4. Wellcome Trust. Sharing research data to improve public health: full joint statement by funders of health research. www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Data-sharing/Public-health-and-epidemiology/WTDV030690.htm.
  5. Lehman R, Loder E. Missing clinical trial data. BMJ 2012; 344:d8158
  6. Hart B, Lundh A, Bero L. Effect of reporting bias on meta-analyses of drug trials: reanalysis of meta-analyses. BMJ 2012; 344:d7202.
  7. Peng RD, Domenici F, Zeger SL. Reproducible epidemiologic research. Am J Epidemiol 2006; 163:783-9
  8. European Medical Research Councils. Implementation of medical research in clinical practice. Forward look. 2011. www.esf.org/publications.html.
  9. Groves T. BMJ Group online evidence to Royal Society call for evidence on science as an open enterprise 2011. http://royalsociety.org/policy/projects/science-public-enterprise/call-for-evidence/
  10. Groves T. BMJ policy on data sharing. BMJ 2010; 340:c564.
  11. Prayle AP, Hurley MN, Smyth AR. Compliance with mandatory reporting of clinical trial results on ClinicalTrials.gov: cross sectional study. BMJ 2012; 343:d7373

Cite this as: BMJ 2012;344:e4383

Competing interests: Both authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf (available on request from the corresponding author) and declare: no support from any organisation for the submitted work; both BMJ (where TG is deputy editor and FG is editor in chief) and BMJ Open (where TG is editor in chief) levy article processing fees to support open access to published research, and at both journals data sharing is strongly encouraged; no other relationships or activities that could appear to have influenced the submitted work.

Provenance and peer review: Commissioned; not externally peer reviewed.

[End BMJ editorial]

We invite you to take a look at some of the data packages in Dryad linked to articles published in BMJ journals, and look forward to seeing many more!

We are experimenting with a nimble new format for our newsletter, in which each item consists of an individual blog post.  All the news items are also available in one PDF document if you’d prefer.

  1. Stakeholder governance.  “The scientific, educational, and charitable mission of Dryad is to promote the availability of data underlying findings in the scientific literature for research and educational reuse. The vision of Dryad is a scholarly communication system in which learned societies, publishers, institutions of research and education, funding bodies and other stakeholders collaboratively sustain and promote the preservation and reuse of data underlying the scholarly literature.”  This Mission Statement is from Dryad’s new Bylaws, which were approved this month by a vote of its Interim Partners. Since its inception, Dryad been guided by the idea that an enduring community resource requires stakeholder governance…
  2. Sustainability planning.  Another important milestone was reached when the organization officially adopted a cost recovery plan to ensure Dryad’s sustainability.  The plan was the result of several years of deliberation among Dryad’s Interim Partners, experts in sustainability, and many prospective Member organizations…
  3. Summer 2011 Interim Board meeting. The governance and cost recovery plan emerged from a consultation process that culminated in a meeting of the Dryad Interim Board in Vancouver, Canada in July 2011. In addition to the governance and sustainability plans, participants also made progress on a number of important policy issues. Several of these bear on what content Dryad will accept…
  4. New funding from the US National Science Foundation. Earlier this year, the NSF, through its Advances in Biological Informatics program, announced a new award of $2.4M over four years to enable Dryad to scale up its technical infrastructure to support the rapidly expanding user base of journals and researchers, ensure that the repository is meeting the needs of that user base…
  5. New integrated journals.  In recent months, more journals have implemented submission integration with Dryad to make data archiving easier for authors.  Technically, the process entails setting up semi-automated communications between Dryad and the manuscript submission system of the journal.  Currently 24 journals have implemented submission integration…
  6. New features. A number of enhancements to Dryad have been made in recent months, including these three that were in high demand from users…

If you do not yet receive our newsletters by email and would like to, please sign up for our low traffic Dryad-announcements mailing list.

“The scientific, educational, and charitable mission of Dryad is to promote the availability of data underlying findings in the scientific literature for research and educational reuse. The vision of Dryad is a scholarly communication system in which learned societies, publishers, institutions of research and education, funding bodies and other stakeholders collaboratively sustain and promote the preservation and reuse of data underlying the scholarly literature.”

This Mission Statement is from Dryad’s new Bylaws, which were approved this month by a vote of its Interim Partners. Since its inception, Dryad been guided by the idea that an enduring community resource requires stakeholder governance, and the Bylaws set out the structure of the membership-based organization by which that will be achieved.

The new governance structure vests financial and legal responsibility with a Board of Directors elected by the Membership. Members may include journals, scientific societies, publishers, funding agencies, universities and any other organization that shares an interest in Dryad’s mission. The twelve Directors serve as individuals, not necessarily affiliated with a Member, and serve – on a voluntary basis – for renewable three-year terms.

A diverse and distinguished list of twenty candidates accepted the nomination to run for the charter Board of Directors in an election held this May. The following twelve individuals were elected to assume office on the 1st of July 2012, and serve terms varying from one to three years.

  • Theodora Bloom, Public Library of Science
  • Lee Dirks, Microsoft Research
  • Simon Hodson, JISC
  • Marcel Holyoak, University of California, Davis
  • Brian Lavoie, OCLC Research
  • William Michener, University of New Mexico
  • Allen J. Moore, University of Georgia
  • Susanna-Assunta Sansone, University of Oxford
  • Eefke Smit, International Association of STM Publishers
  • Todd Vision, Biology Dept., University of North Carolina at Chapel Hill
  • Michael Whitlock, University of British Columbia

The first face-to-face Board Meeting will be held this July in Durham, North Carolina, and the first annual Members Meeting will be held in May 2013. More background on the history and current status of Dryad’s governance is available at http://wiki.datadryad.org/Governance.

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