Feeds:
Posts
Comments

Archive for June, 2012

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!

Read Full Post »

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.

Read Full Post »

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, 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.

Read Full Post »

An important milestone was reached when the Dryad organization officially recently 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.

The plan identifies three primary funding sources. First are deposit fees, and there are several ways in which they may be paid:

  • A journal or publisher may agree to pay an annual fee based on the number of articles it publishes annually, in anticipation that a substantial fraction will have data deposited in Dryad.
  • An organization (typically, but not necessarily, a journal or publisher) may pay a fixed fee per data deposited. Vouchers may be purchased for bulk purchases in advance, or organizations may be regularly billed after deposits are received.
  • If the fee is not paid through the journal, society, publisher, or other organization, authors may pay the deposit fee at the time of deposit.

The deposit fee will vary among these options depending on transaction costs. It is expected that a Member-discounted prepaid voucher will cost approximately $50 USD.  Members will be entitled to receive a 10% discount.

The rationale for deposit-fees is several-fold.  First, collecting revenue upfront allows Dryad to make the data freely available to users and ensure that preservation costs will not be lacking down the road.  With a repository of sufficient size, most non-fixed costs are due to new deposits, and are incurred at the time of deposit.  Charging deposit fees ensures that revenues will scale with expenses and that funds are available to the repository when they are needed.  Furthermore, there are many different parties making deposits, and the number of deposits from different journals, institutions, investigators, etc., varies widely. Deposit fees have the virtue of distributing the costs among the many parties so that the amount required by each party is relatively small and varies in proportion to usage.

Another source of revenue will be annual membership fees, expected to be $1000 USD annually, which will confer voting rights, discounted deposit fees, participation in Annual Meetings, and other benefits.

Deposit fees and membership fees are intended to cover the operating costs of the repository. The third revenue source, funding from grants and charitable organizations, will be used for research, development, and new initiatives.  It is expected that this plan will be implemented in parallel with an endowment campaign, which may be used to reduce deposit fees, invest in new technologies, and help assure long-term sustainability. More details about the plan are available at http://wiki.datadryad.org/Business_Plan_and_Sustainability.

Read Full Post »

Dryad’s new governance structure 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.  This was the third and final meeting of this temporary governing body. Over 25 representatives from a diversity of journals, societies, publishers and other organizations met at the University of British Columbia to review progress and chart the next steps for Dryad.

Vancouver maple tree, courtesy of Marcel Holyoak, via Flickr

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:

  • Software: Dryad is intended to provide a repository for code only where it does not otherwise have a better home. It is expected that Dryad will be used primarily for snapshots or “one-off” scripts that would otherwise be lost, rather than the maintenance of ongoing software projects that would be better hosted by a public version control system.
  • Other integral and supplementary materials:  Dryad will accept the full range of content that is currently hosted by the journal/publisher as Supplemental Online Material, and not restrict the repository contents strictly to data. This option will be provided to those journals or publishers that wish to take advantage of it.  Whether it be software, data, or other material, authors will still be asked to release rights to the content under the terms of CCZero.
  • Qualifying publications:  All content in Dryad must be documented by a publication. The Interim Board expanded the definition of qualifying publications to include not just those that have undergone peer review, but any legitimate publication with expert vetting, such as a doctoral thesis.

The report of the meeting is available here.   We extend particular thanks for the success of the meeting to the members of the interim Executive Committee: Marcel Holyoak, William Michener, Allen Moore and Michael Whitlock (chair and host at UBC).

Read Full Post »

A number of enhancements to the repository have been made in recent months, including these three that were in high demand from users:

  • First, we have modified our submission process to enable the data to be deposited prior to editorial review of the manuscript. Journals that integrate manuscript and data submission at the review stage can now offer their editors and peer reviewers anonymous access to the data in Dryad while the manuscript is in review. This option is currently being used by several of our partner journals, BMJ Open, Molecular Ecology, and Systematic Biology, and is available to any existing or future integrated journal. Note: authors still begin their data deposit process at the journal.
  • Second, when authors submit data associated with previously published articles, they can pull up the article information using the article DOI or its PubMed ID, greatly simplifying the deposition process for legacy data.
  • Third, Dryad now supports versioning of datafiles. Authors can upload new versions of their files to correct or update the original file. Once logged in to their Dryad account, the My Submissions option appears under My Account in the left side-menu. Prior unfinished and completed submissions are listed; selecting an archived submission allows the author to add a new file.  Note that the earlier versions of the file will still be available to users, but the metadata may be modified to reflect the reason for the update. The DOIs will be appended with a number (e.g., “.1”, “.2”) so that each version can be uniquely referenced.  By default, users will be shown the most current version of each datafile.  They will be notified of the existence of any previous/subsequent versions.
  • Access and download statistics have been displayed for content in the repository since late 2010; Dryad now displays the statistics for an article’s data together on one page so you can see at a glance how many times the page has been viewed and how many times each component data file has been downloaded. Check out this example from Evolutionary Applications.

Read Full Post »

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. Journals that have been added in the past year include:

  • BMJ Open, published by the BMJ Group
  • Ecological Monographs, published by the Ecological Society of America
  • Evolutionary Applications, published by Wiley-Blackwell
  • Heredity, published by the Genetics Society with Nature Publishing Group
  • Journal of Fish and Wildlife Management, published by the US Fish and Wildlife Service
  • Journal of Paleontology and Paleobiology, both published by The Paleontological Society with Allen Press
  • PLoS Biology, published by the Public Library of Science
  • Systematic Biology, published by the Society of Systematic Biologists with Oxford University Press
  • ZooKeys, along with seven other journal titles from Pensoft Publishers.

Thanks to the growing number of integrated journals, growing awareness of Dryad, and the importance of data archiving, the rate at which we are receiving deposits continues to grow steadily.  Dryad currently holds over 1700 data packages, associated with articles in well over 100 different journals.  About three quarters of submissions are from the minority of journals for which submission integration is in place.

Editors and publishers interested in implementing integration may review our documentation and contact Dryad or fill out our Pre-Integration Questionnaire to begin the integration process. There is no charge for implementing integration with Dryad.

Read Full Post »

Follow

Get every new post delivered to your Inbox.

Join 7,752 other followers