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Posts Tagged ‘journals’

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.

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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.

SciData_new_logo

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.

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We are pleased to announce that Elementa is the latest journal to integrate submission of manuscripts with data to Dryad.  Elementa’s integration with Dryad means that all authors will be invited to archive the data supporting the conclusions in their article, and their process of depositing data files has been simplified by the behind-scenes-coordination between the journal and the repository. Authors will be invited to submit data to Dryad when their manuscript is accepted, and will have the option to set a one-year embargo on the availability of their data files.

The journal has a strong data policy, requiring “all major datasets associated with an article to be made freely and widely available.” The journal is also a Dryad member, and will be covering the charges for its authors when Dryad begins assessing Data Publishing Charges (DPC) on September 1.

Elementa: Science of the Anthropocene is a new open access scientific journal publishing original research reporting new knowledge of the Earth’s physical, chemical, and biological systems.

logo The journal is a nonprofit collaborative involving BioOne, Dartmouth, the Georgia Institute of Technology, the University of Colorado, the University of Michigan, and the University of Washington. Elementa is comprised of six inaugural knowledge domains: Atmospheric Science, Earth and Environmental Science, Ecology, Ocean Science, Sustainable Engineering, and Sustainability Transitions.

The journal is now welcoming article submissions, and the first articles will be published in September.

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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.

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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.

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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.

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Christopher Pirrone excavating an odontocete skull (photo by Robert Boessenecker)

Perhaps it’s understandable that paleontologists are committed to preserving the scientific record, since they spend a lot of time and energy finding and extracting shreds of evidence millions of years old.  Now, thanks to a partnership between Dryad and The Paleontological Society announced last year [1], coupled with strong data archiving policies adopted by two of its journals (Paleobiology and the Journal of Paleontology), a rich trove of data will be available for future researchers to unearth from Dryad.

For both journals, authors are being instructed to deposit the underlying data at the time their manuscript is submitted, so that editors and referees will be able to review it prior to acceptance.  Once published on Dryad, the data will be independently discoverable and citable, while at the same time prominently linked both to and from the original article.  Researchers are able to track the reuse impact of their data, independent of the citation impact of their article, by monitoring downloads from Dryad.

Preserved for ages.

Smilodon, by Charles Knight (1905), from a mural at the American Museum of Natural History.

Here’s an example from a recent issue of Paleobiology to sink your teeth into:

Article: Meachen-Samuels JA (2012) Morphological convergence of the prey-killing arsenal of sabertooth predators. Paleobiology 38(1): 1-14. doi:10.1666/10036.1

Data: Meachen-Samuels JA (2012) Data from: Morphological convergence of the prey-killing arsenal of sabertooth predators. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h58q6

References:

[1]  Callaway E (2011) Fossil data enter the web period. Nature 472, 150. http://dx.doi.org/10.1038/472150a

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