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We are delighted to announce the integration of four new journals: Ecography, Journal of Avian Biology, Nordic Journal of Botany, and Oikos.

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The Nordic Society Oikos, which supports scientific research in ecology and related disciplines and to stimulate and enhance communication between stakeholders in ecological research in the Nordic countries and beyond, owns these journals, and is generously sponsoring Data Publication Charges on behalf of its authors. The Oikos Editorial Office, based in the Department of Biology at Lund University, manages the publication of these journals in partnership with Wiley. For all four journals, authors should submit the data to Dryad after the manuscript has been accepted.

Please see here for more information about how your journal can integrate manuscript and data submission to Dryad,

 

Dryad has been proud to support integrated data and manuscript submission for PLOS Biology since 2012, and for PLOS Genetics since 2013.  Yet there are over 400 data packages in Dryad from six difFeatured imageferent PLOS journals in addition to two research areas of PLOS Currents. Today, we are pleased to announce that we have expanded submission integration to cover all seven PLOS journals, including the two above plus PLOS Computational BiologyPLOS MedicinePLOS Neglected Tropical DiseasesPLOS ONE, and PLOS Pathogens.  

PLOS received a great deal of attention when they modified their Data Policy in March providing more guidance to authors on how and where to make their data available and introducing Data Availability Statements. Dryad’s integration process has been enhanced in a few ways to support this policy and also the needs of a megajournal like PLOS ONE.  We believe these modifications provide an attractive model for integration that other journals may wish to follow. The key difference for authors who wish to deposit data in Dryad is that you are now asked to deposit your data before submitting your manuscript.

  1. PLOS authors are now asked to provide a Data Availability Statement during initial manuscript submission, as shown in the screenshot below. There is evidence that introducing a Data Availability Statement greatly reinforces the effectiveness of a mandatory data archiving policy, and so we expect this change will substantially increase the availability of data for PLOS publications.  PLOS authors using Dryad are encouraged to provide the provisional Dryad DOI as part of the Data Availability Statement.
  2. PLOS authors are now also asked to provide a Data Review URL where reviewers can access the data, as shown in the second screenshot. While Dryad has offered secure, anonymous reviewer access for some time, the difference now is that PLOS authors using Dryad will be able to enter the Data Review URL  at the time of initial manuscript submission.
  3. In addition to these visible changes, we have also introduced an Application Programming Interface (API) to facilitate behind-the-scenes metadata exchange between the journal and the repository, making the process more reliable and scalable. This was critical for PLOS ONE, which published 31,500 articles in 2013.  Use of this API is now available as an integration option to all journals as an alternative to the existing email-based process, which we will continue to support.

PLOS Data Availability Statement interface

PLOS Data Review URL interface

The manuscript submission interface for PLOS now includes fields for a Data Availability Statement and a Data Review URL.

If you are planning to submit a manuscript but are unsure about the Dryad integration options or process for your journal, just consult this page. For all PLOS journals, the data are released by Dryad upon publication of the article.  Should the manuscript be rejected, the data files return to the author’s private workspace and the provisional DOI is not registered.  Authors are responsible for paying Data Publication Charges only if and when their manuscript is accepted.

Jennifer Lin from PLOS and Carly Strasser from the California Digital Library recently offered a set of community recommendations for ways that publishers could promote better access to research data:

  • Establish and enforce a mandatory data availability policy.
  • Contribute to establishing community standards for data management and sharing.
  • Contribute to establishing community standards for data preservation in trusted repositories.
  • Provide formal channels to share data.
  • Work with repositories to streamline data submission.
  • Require appropriate citation to all data associated with a publication—both produced and used.
  • Develop and report indicators that will support data as a first-class scholarly output.
  • Incentivize data sharing by promoting the value of data sharing.

Today’s expanded and enhanced integration with Dryad, which inaugurates the new Data Repository Integration Partner Program at PLOS, is an excellent illustration of how to put these recommendations into action.

We are happy to announce two new journals, Royal Society Open Science and Ecological Applications, that will be making it easy for authors to archive their data in Dryad through integration of manuscript and data submission.

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Royal Society Open Science is a new open access journal. It is the first title from The Royal Society that welcomes contributions from across science, engineering and mathematics, and the ninth to integrate with Dryad.  The Royal Society will sponsor the Data Publishing Charges on behalf of its authors.

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Ecological Applications is the second integrated journal published by the Ecological Society of America, and it comes on the heels of  a strengthened data policy that came into force at the beginning of 2014.

For both journals, authors submit data to Dryad upon acceptance of the manuscript.  For a full list of integrated journals, with instructions for each one on when to submit, whether authors may elect to embargo their data, and whether Data Publishing Charges are sponsored, please see here.

Dryad welcomes submission integration with scientific journals irrespective of whether the organization is signed up for a payment plan or is a member of Dryad. The submission integration process works with many different online manuscript processing systems. It is lightweight and customizable to each journal’s needs. Please contact us if you would like to consider submission integration for your journal.

Molecular Ecology cover imageWe are pleased to report that Molecular Ecology is now the first journal to surpass 1000 data packages in Dryad! Our latest featured data package is the one that took Molecular Ecology past the goalposts:

  • Bolnick D, Snowberg L, Caporaso G, Lauber C, Knight R, Stutz W (2014) Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Molecular Ecology doi:10.1111/mec.12846
  • Bolnick D, Snowberg L, Stutz W, Caporaso G, Lauber C, Knight R (2014) Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Dryad Digital Repository doi:10.5061/dryad.2s07s

Why so many data packages from Molecular Ecology?  It is likely due to a few factors.  One, Molecular Ecology publishes a lot of papers (445 in 2012 according to Journal Citation Reports) and have had integrated data and manuscript submission with Dryad since 2010.  Two, the field works with many datatypes for which no specialized repository exists.  Three, Molecular Ecology not only began requiring data archiving in 2011 when it adopted the Joint Data Archiving Policy, but actually goes beyond JDAP by requiring a completed data availability statement in each article, something that managing editor Tim Vines and his colleagues have shown to be associated with very high rates of data archiving. Four, since Dryad introduced Data Publishing Charges, Molecular Ecology has been sponsoring those charges on behalf of its authors.

Other journals looking to support data archiving in their fields would do well to look at Molecular Ecology as a model.

Dryad is seeking an energetic and enthusiastic Executive Director, ideally with experience in scientific or biomedical research, librarianship, or publishing, to oversee development and operation of the organisation during a period of rapid growth and transformation. The role reports to the Board of Directors. Externally, the postholder will be responsible for building relationships with stakeholders, customers and users of the Dryad Digital Repository. Internally, key responsibilities include organisational leadership and ensuring Dryad meets its objectives through sound financial management and oversight of day-to-day operations, with the support of a small but growing staff.  Review of applications will begin by September 1, 2014 and continue until the position is filled. For details please see the full position description and for inquiries please contact director@datadryad.org.

A number of notable publications have been added to the growing list of those integrating submission of data and manuscripts with Dryad.

The recently adopted Data Policy of Royal Society Publishing now requires that data sets “be deposited in an appropriate, recognized, publicly available repository” and that authors “disclose upon submission of the manuscript any restrictions on the availability of research materials or data.” To support this policy, the Royal Society now sponsors the Data Publication Charge to Dryad for data associated with any of its publications Proceedings of the Royal Society, Proceedings B, the Royal Society’s flagship biological research journal, has joined Biology Letters in integrating submission with Dryad.  Currently, submission of data occurs prior to manuscript review for Proceedings B, and following acceptance for Biology Letters.  Watch this space for further efforts to support the data archiving needs of Royal Society Publishing.

BMCEcologyBMCEvolBiology

In an editorial entitled ‘An open future for ecological and evolutionary data?’, recently published jointly in BMC Ecology and BMC Evolutionary Biology, authors Amye Kenall, Simon Harold and Christopher Foote announce the integration of manuscript submission for these two journals with Dryad in order “to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors.”  Now that the technical work has been accomplished for these two journals, submission integration can be easily extended to other BMC series titles at the request of the editors.

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Scientific Data is a newly launched open access publication from Nature Publishing Group that aims to promote the accessibility and reuse of scientifically valuable data sets. This is supported by both a strong data deposition policy and a novel publication type called a Data Descriptor.

Data Descriptors will provide detailed descriptions of the experiments and procedures involved in generating important datasets, including essential information needed for scientists to assess the technical quality of the data, reproduce key methods or analysis workflows, and ultimately reuse the data to address important research questions. In addition, every publication at Scientific Data will be supported by metadata describing key properties of the experiments and resulting data, which will be checked by an in-house curator and released in the ISA-tab format, and hopefully other standard formats in the future. These metadata will aid data mining, and will help scientists find and reuse high-quality datasets stored across multiple data repositories.

NPG sponsors data submissions associated with Scientific Data, and data are submitted to Dryad prior to review.

Together with a number of previously integrated journals from German Medical Science and Pensoft Publishers, on subjects ranging from subterranean biology to reconstructive surgery, the total number of titles now integrated with Dryad exceeds 50. Authors may consult this list to see which journals are integrated, when to submit data (either before review of after acceptance), whether the journal allows an optional data embargo, and whether Data Publication Charges are sponsored for that publication.Submission integration is a free service, and can be implemented with a wide variety of manuscript submission systems. We encourage publishers and editors to contact us about integration of additional titles, and we encourage authors to let editors know if this is a feature that they would value.

The following is a guest post from Tom Jefferson of The Cochrane Collaboration, Peter Doshi of the University of Maryland and Carl Heneghan from the University of Oxford. We asked them to tell the story behind their recent Cochrane systematic review [1] and dataset in Dryad [2] which holds valuable lessons about the evidence-base on which major public health recommendations are decided.  -TJV1918 Influenza Poster

In the late 2000s, half the world was busy buying and stockpiling the neuraminidase inhibitors oseltamivir (Tamiflu, Roche) and zanamivir (Relenza, GSK) in fear of an influenza pandemic.

The advice to stockpile for a pandemic and also use the drugs in non-pandemic, seasonal influenza seasons came from such august bodies as the World Health Organization (WHO), the US Centers for Disease Control and Prevention (CDC) and its European counterpart, the ECDC. However, they were stockpiling on the basis of an unclear rationale, mixing the effect of the antiviral drugs on the complications of influenza (mainly pneumonia and hospitalizations) and their capacity to slow down viral spread giving time for vaccines to be crash produced and deployed.

It has since become clear that none of these parties had seen all the clinical trial evidence for these drugs. They had based their recommendations on reviews of “the literature” which sounds impressive, but in fact refers to short trial reports published in journal articles rather than the underlying detailed raw data. For example, key assumptions of antiviral performance found in the US national pandemic plan trace back to a six page long journal article written by Roche which reported on a pooled-analysis of 10 randomized trials of which only 2 have ever been published.

In contrast, each of the corresponding internal clinical study reports for these 10 trials runs thousands of pages (for background on what clinical study reports are, see here.) Despite the stockpiling, these reports have never been reviewed by CDC, ECDC, or WHO. The WHO and CDC both refused to answer our questions on the evidence base for their policies.

Our Cochrane systematic review of neuraminidase inhibitors, funded by the National Institute for Health Research in the UK, was based on analysis of the full clinical study reports for these drugs, not short journal publications. We obtained these reports from the European Medicines Agency, Roche, and GlaxoSmithKline.  It took us nearly four years to obtain the full set of reports. The story of how we got hold of the complete set of clinical trials with no access restrictions is told in our essay “Multisystem failure: the story of anti-influenza drugs”.

With the publication of our review, we are making all 107 full clinical study reports publicly available. If you disagree with our findings, if you want to carry out your own analysis or if you are just curious to see what around 150,000 pages of data look like, they are one click away. Now the discussion about how well these drugs work can happen with all parties able to independently analyze all the trial evidence. This is called open science.

Be aware that there are some minimal redactions carried out by GSK and Roche. They did this to protect investigator and participant identity. While protecting participant identity is understandable, the EMA carries a different view towards protecting investigator identity: “names of experts or designated personnel with legally defined responsibilities and roles with respect to aspects of the Marketing Authorisation dossier (e.g. QP, QPPV, Clinical expert, Investigator) are included in the dossier because they have a legally defined role or responsibility and it is in the public interest to release this data”.

References

  1. Jefferson T, Jones MA, Doshi P, Del Mar CB, Hama R, Thompson MJ, Spencer EA, Onakpoya I, Mahtani KR, Nunan D, Howick J, Heneghan CJ (2014) Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children. Cochrane Database of Systematic Reviews, online in advance of print. doi:10.1002/14651858.CD008965.pub4
  2. Jefferson T, Jones MA, Doshi P, Del Mar CB, Hama R, Thompson MJ, Spencer EA, Onakpoya I, Mahtani KR, Nunan D, Howick J, Heneghan CJ (2014) Data from: Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children. Dryad Digital Repository. doi:10.5061/dryad.77471
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