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Archive for the ‘Journals’ Category

Chain link fence with highway in backgroundDryad is a curated, non-profit, general-purpose repository specifically for data underlying scientific and medical publications — mainly journal articles. As such, we place great importance on linking data packages to the articles with which they are associated, and we try our best to encourage authors and journals to link back to the Dryad data from the article, ideally in the form of a reference in the works cited section. (There’s still a long way to go in this latter effort; see this study from 2016 for evidence).

Submission integration provides closer coordination between Dryad and journals throughout the publishing workflow, and simplifies the data submission process for authors. We’ve already implemented this free service with 120 journals. If you’re interested in integrating your journal, please contact us.

We’re excited to share a few recent updates that are helping to make our data-article linkages more efficient, discoverable, and re-usable by other publishers/systems.

The Automated Publication Updater

One of the greatest housekeeping challenges for our curation team lies in finding out when the articles associated with Dryad data packages become available online. Once they do, we want to add the article citation and DOI link to our record as quickly as possible, and to release any data embargoes placed “until the article appears.” Historically, we’ve achieved this through a laborious patchwork of web searches, journal alert emails, and notifications from authors or editors themselves.

But over the past year or so, we’ve built and refined a webapp that we call the APU (or Automated Publication Updater). This super-handy tool essentially compares data packages in the Dryad workflow with publication metadata available at Crossref. When a good match is found, it automatically updates article-related fields in the Dryad record, and then sends our curation team an email alert so they they can validate the match and finalize the record. The webapp can be easily run by curators as often as needed (usually a few times a week).

While the APU doesn’t find everything, it has dramatically improved both efficiency with which we add article information and links to Dryad records — and our curators’ happiness levels. Big win. (If you’re interested in the technical details, you can find them on our wiki).

Scholix

Dryad is also pleased to be a contributor to Scholix, or Scholarly Link Exchange, an initiative of the Research Data Alliance (RDA) and the World Data System (WDS). Scholix is a high-level interoperability framework for exchanging information about the links between scholarly literature and data.

  • The problem: Many disconnected sources of scholarly output, with different practices including various persistent identifier (PID) systems, ways of referencing data, and timing of citing data.
  • The Scholix solutionA standard set of guidelines for exposing and consuming data-article links, using a system of hubs.

Here’s how it works:

  1. As a DataCite member repository, Dryad provides our data-publication links to DataCite, one of the Scholix Hubs. 
  2. Those links are made available via Scholix aggregators such as the DLI service
  3. Publishers can then query the DLI to find datasets related to their journal articles, and generate/display a link back to Dryad, driving web traffic to us, increasing data re-use, and facilitating research discovery.

Crossref publishers, DataCite repositories/data centers, and institutional repositories can all participate — information on how is available on the Scholix website.

Programmatic data access by ISSN

Did you know that content in Dryad is available via a variety of APIs (Application Program Interfaces)? Details are available at the “Data Access” page on our wiki.

The newest addition to this list is the ability to access Dryad data packages via journal ISSN. So, for example, if you wanted access to all Dryad content associated with the journal Evolution Letters, you would format your query as follows:

https://datadryad.org/api/v1/journals/2056-3744/packages

If you’re a human instead of a machine, you might prefer to visit our “journal page” for Evolution Letters:

https://datadryad.org/journal/2056-3744

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Dryad is committed to values of openness, collaboration, standardization, seamless integration, reduction of duplication and effort, and increased visibility of research products (okay, data especially). The above examples are just some of the ways we’re working in this direction.

If you’re part of an organization who shares these values, please contact us to find out how you can be part of Dryad.

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oupDryad is very pleased to announce more integrations from charter member and partner Oxford University Press Journals. Oxford University Press (OUP) publishes over 300 journals, many with the support of learned societies. As part of Oxford University, OUP brings a rich history of working with researchers.

OUP has integrated seven more journals with Dryad, all of which can provide secure links to data during the peer review process:

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  • Behavioral Ecology – published on behalf of  The International Society for Behavioral Ecology, Behavioral Ecology publishes studies on the whole range of behaving organisms, including plants, invertebrates, vertebrates, and humans. Data publication is sponsored for Behavioral Ecology authors.
  • BioScience – published on behalf of the American Institute of Biological Sciences, BioScience has been publishing current research in Biology since 1964.
  • Environmental Epigenetics is an open access journal that publishes research in any area of science and medicine related to the field of epigenetics.
  • Toxicological Sciences is the official journal of the Society of Toxicology and publishes influential research in toxicology. Data publication is sponsored for authors for Toxicological Sciences.
  • Journal of Urban Ecology is an open access journal which covers all aspects of urban environments. This includes the biology of the organisms that inhabit urban areas, the diversity of ecosystem services, and human social issues encountered within urban landscapes.
  • Virus Evolution serves the community of virologists, evolutionary biologists and ecologists who are interested in the genetic diversity and evolution of non-cellular forms of life.
  • Work, Aging and Retirement reflects a broad community of professionals in the fields of psychology, sociology, economics, gerontology, business and management, and industrial labor relations.

Integration with Dryad ensures bidirectional links between the article and the data, and increased visibility for both. It also simplifies the process of data submission for authors. All data in Dryad is reviewed by professional curators who perform basic checks to ensure discoverability and proper metadata, and becomes freely accessible online once approved.

Oxford University Press is increasing its commitment to authors and to quality by making it easy to publish datasets alongside the manuscript, and by allowing data to be available during the peer review process.

We’re delighted to build our partnership with Dryad by integrating this set of OUP journals. Providing authors with a simple and user-friendly route to data sharing helps to increase transparency and reproducibility of published research, and ultimately must be good for science. We hope to integrate more of our journals in the near future.

– Jennifer Boyd, Senior Publisher Life Science Journals, OUP

To learn more about journal integration with Dryad and DPCs, contact us.

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We are delighted to announce the launch of a new partnership with The Company of Biologists to support their authors in making the data underlying their research available to the community.

COBNewLogo300dpiThe Company of Biologists is a not-for-profit publishing organization dedicated to supporting and inspiring the biological community. The Company publishes five specialist peer-reviewed journals:

The Company of Biologists offers further support to the biological community by facilitating scientific meetings, providing travel grants for researchers and supporting research societies.

Manuscript submission for all COB journals is now integrated with data submission to Dryad, meaning COB authors can conveniently submit their data packages and manuscripts at the same time. Dryad then makes the data securely available to journal reviewers, and releases them to the public if/when the paper is published.

We congratulate The Company of Biologists on taking this important step to help facilitate open data. To learn more about how your organization or journal can partner with Dryad, please contact us.

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UCP logoDryad is very pleased to announce a new partnership with the University of Chicago Press – Journals Division. Founded in 1890, Chicago is one of the oldest and currently the largest continuously operating university press in the United States. Chicago has recently integrated two additional journals with Dryad: Physiological and Biochemical Zoology (PBZ) and International Journal of Plant Sciences (IJPS) and is sponsoring Data Publication Charges (DPCs) for both titles. PBZ and IJPS join sister publication, The American Naturalist, a Dryad partner since its inception.

Integration with Dryad

  • Ensures bidirectional links between the article and the data, and increased visibility for both
  • Simplifies the process of data submission for authors
  • Takes advantage of Dryad’s professional curators who perform basic checks to ensure discoverability and proper metadata
  • Ensures that the data is freely accessible once the article becomes available online

Physiological and Biochemical Zoology publishes original research in the areas of animal physiology and biochemistry. PBZ focuses on ecological, evolutionary and behavioral aspects of morphological, physiological, and biochemical mechanisms. PBZ’s integration will allow authors to make their data available to journal editors during peer review.

The International Journal of Plant Sciences has been publishing plant science research since 1875. IJPS covers a wide range of topics including genetics and genomics, developmental and cell biology, biochemistry and physiology, morphology and anatomy, systematics, evolution, paleobotany, ecology, and plant-microbe interactions. IJPS will accept data from authors at the time of article acceptance.

The University of Chicago Press – Journals Division is increasing its commitment to authors and the STM field by making it easy to publish datasets alongside the manuscript, and by taking the extra step of covering the cost of data publication on behalf of authors. To learn more about journal integration with Dryad and DPCs, contact us.

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We are delighted to announce the integration of three new journals: The Bone & Joint Journal, Bone & Joint Research and Bone & Joint360.

BJJBJRBJ360

The British Editorial Society of Bone & Joint Surgery is a not-for-profit charity formed in 1953 for “the advancement and improvement of education in orthopaedic surgery and allied branches of surgery,” achieved through publication of The Bone & Joint Journal (formerly known as JBJS (Br)). With all three 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.

 

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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,

 

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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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