Archive for the ‘New features’ Category

Credit: adamthelibrarian, from Flickr

This is an important month, because a host of our partner journals are implementing new policies on data archiving, and, in the U.S., the National Science Foundation is asking its new grantees to have explicit data management plans.  There are over 1000 data files from over 50 journals now in Dryad, and much of this content has been submitted only within the past year. Clearly, Dryad’s role in supporting the growing data archiving mandates from journals and funders continues to expand.

New Features
In the past few months, several new features have been added to Dryad.  Users can now save an incomplete submission and come back later to complete it.  They can see a listing of their completed and in progress submissions.  Users can download data citations to their favorite bibliography management programs and upload them to their favorite social bookmarking tools.  A new “faceted search” interface allows users to find data more easily, and also displays related content in other repositories, including ecological and environmental science data (from the Knowledge Network for Biocomplexity) and phylogenetic data (from TreeBASE). To provide an early indication of scientific impact, users can see how often data have been viewed and downloaded.

An important new feature is “handshaking”, which is what we call the process whereby authors upload some of their data to Dryad, and the information is conveyed behind-the-scenes to a specialized repository. The aim of handshaking is to reduce the time and effort need to deposit data when there are different repositories managing different aspects of the data.  Handshaking also enables persistent linkages among data in the different repositories. As a first foray into handshaking, we now offer users the option of initiating a deposit in TreeBASE, the primary repository for published phylogenetic data, whenever a NEXUS file is uploaded to Dryad.  Alternatively, the option is available to deposit in another repository first, and report the identifiers to Dryad to ensure that users can find all the data relevant to a given article.  We will be working in the months ahead to handshake with other specialized repositories required by our partner journals.

See our recent blog post about these features for more details.

Data Deposit in Three Easy Steps: The Movie
Are you looking for a way to show a colleague how straightforward data archiving can be?  We’ve added a short (2-minute) video to the site that walks users through the deposit process in three easy steps.  The video also available at SciVee.

Journals Implement Joint Data Archiving Policy
Starting this month, a number of Dryad partner journals have implemented a Joint Data Archiving Policy that requires, as a condition of publication, that authors deposit the data underlying their article in a public repository.  Some of the journals implementing this policy include: The American Naturalist, Evolution, Evolutionary Applications, Heredity, Journal of Evolutionary Biology, and Molecular Ecology. A recent TREE article by Michael Whitlock suggests how “data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving.”

A growing number of journals now integrate their submission process with Dryad, meaning that the repository and journal exchange information to facilitate the author’s data deposition process and to ensure persistent linkage between articles and data. The current list includes The American Naturalist, The Biological Journal of the Linnean Society, Evolution, Journal of Evolutionary Biology, Journal of Heredity, Molecular Ecology, and Molecular Ecology Resources. And more are on the way (stay tuned).

NSF Data Management Plan Mandate
Starting this month, the U.S. National Science Foundation is requiring grant applicants to provide a data management plan describing how data will be collected, preserved and made available, and these plans will be subject to peer review.  We encourage applicants to leverage Dryad in their data management plans as a solution for the long-term preservation and dissemination of the data associated with their publications.  There are some pointers to resources for data management planning on the Dryad website.

Dryad UK Project
The Joint Information Science Committee (JISC) in the UK has made an award to Dryad and through Oxford University and the British Library to expand the scope of the journals involved, including into the areas of infectious disease and epidemiology, and to create a UK mirror of Dryad.  More information is here and at the Dryad UK site.

New Twitter Feed for Data Deposits
Interested in keeping up with new data available in Dryad?  Follow our Twitter feed (@datadryadnew) or subscribe to our RSS feed. We also Tweet general news about the repository and the world of data science as @datadryad.

Browse and search the repository at http://datadryad.org/
Follow Dryad on Twitter http://twitter.com/datadryad

This blog post is the first issue of the Dryad newsletter, summarizing recent achievements and milestones of the data repository.  If you’d like to receive future newsletters by email, please sign up for the Dryad Users mailing list.

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Are you curious about what’s involved in depositing data in Dryad? looking for a quick way to show colleagues how straightforward data archiving can be?  Dryad’s new 2-minute video demonstrates the data deposit process from start to finish.

How to deposit data in Dryad

The video is embedded on the Dryad website, and also available on SciVee. Feel free to link to it and share it with colleagues.

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Ever wonder what happens to your Dryad data behind the scenes? Here’s a quick overview.

Once a depositor has uploaded their data files and finalized their submission, the Dryad curator is notified of the new content. The curator looks at the uploaded files to make sure they really do contain data (and not, say, the article manuscript or pictures of kittens). The curator then exerts some quality control on the metadata, the description of the article and data files. She corrects errors, such as typos or formatting tags that are displaying incorrectly, and may enrich the metadata, by adding taxon name keywords, for example. Advanced metadata enrichment issues include the tricky realm of name authority control, which ensures that all works by a given author are gathered together despite the varying forms of their name.

Once the curator approves the submission, the metadata description of the data goes live in the repository. The status of the data files themselves depends upon the embargo options selected by the depositor. Dryad DOIs (Digital Object Identifiers) are sent to the depositor and, in the case of our integrated partner journals, to the journal editors, so that they can be included in all forms of the final published article, and allow readers of the article to find the supporting data.

After the article is published, the curator adds complete article citation information, including a hyperlinked article DOI, to the Dryad record, and updates any data file embargoes, if needed.

The outcome is data files, which

  • are securely deposited in the repository, and linked to the journal article,
  • have a unique, permanent identifier that can be cited, and
  • can be discovered independently of the article, as well as through the article.

Additionally, authors can now track the views and downloads of their data files.   Dryad displays the number of times the data package has been viewed, and the number of times each component data file has been both viewed and downloaded.

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We’ve created a new Twitter feed for announcing all new data packages added to Dryad.  It’s @datadryadnew — follow it if you want to keep an eye on what is going in to the repository.

Our @datadryad feed is also available, for updates on the Dryad repository and data sharing in general.

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The Dryad team is pleased to announce a new release (1.7)  with several powerful and much-requested features.

Dryad’s revamped submission system enables partial submissions to be saved so that authors can complete their submissions over multiple sessions, when needed. This has been the number one request from users.

credit: US National Archives

“Handshaking” is the process of coordinated data submission so that authors can use Dryad’s easy submission interface to launch a submission process at one or more specialized repositories. This not only reduces overall deposit time, but enables persistent linkages among data in the different repositories.  As a first foray into handshaking, we are offering users the option of using Dryad to send relevant data to TreeBASE, a primary repository for published phylogenetic data.

Now, users can save Dryad data citations to their favorite bibliography management program, and can also share them using any number of online social bookmarking tools.  Applications supported include EndNote, Reference Manager, ProCite, BibDesk, LaTeX, RefWorks, Zotero, Mendeley, delicious, Connotea, Twitter, and Facebook.

Wondering how many times your data in Dryad has been viewed or downloaded?  Dryad now displays access and download statistics for all data packages and each data file. More detailed statistics are coming in a future release.

Dryad’s faceted search interface can now be used to find related content in other repositories. Searching Dryad, users can now find related content from the Long Term Ecological Research network, which hosts a wide array of ecological and environmental science data, as well as phylogenetic data from TreeBASE.


Please explore these new features and let us know what you think  (either by email or through our feedback form).

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We are happy to announce the new quarterly release of Dryad this week.  Some of the most visible enhancements in this version include:

  • One can launch a new search for data from any page using a ‘simple search’ text box.
  • All data packages and data files are now assigned DOIs.
  • The options for when to publish the data have been expanded.  Now authors can now choose to publish their data immediately upon deposit, once the article is published (default), or 1 yr post-publication (embargo).
  • The submission system “timeout” has been extended to 4 hrs to prevent browser sessions expiring before data submission is complete.  (The subsequent release will allow users to save, and return to, incomplete submissions).
  • And while less visible, the production servers for Dryad are now hosted by the North Carolina State University Library, with replication and backup at NESCent.

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In order to make data submission to Dryad as easy as possible for authors, the system piggybacks in an innovative way on the journal submission process.  The key is that most authors will be submitting their data to Dryad immediately after they learn that their final manuscript has been accepted by the journal.  Through behind-the-scenes communication with the journal, Dryad will already know the “vital information” about that paper before the author comes to Dryad to submit data.  This saves them from the laborious and error-prone task of filling in the paper details at Dryad.  We call this process “submission integration”, and it is one of the fundamental services provided to partner journals.

Dryad submission integration screenshot

A screenshot of the Dryad submission page.

Most journals employ one of a small number of manuscript management software systems to interact with authors, editors and reviewers. These software systems regularly employ customizable email form letters to communicate among the various parties.  Through emails that are automatically sent, and automatically processed upon receipt, Dryad can ensure that authors need not re-enter data that is already available to the journal, that the journal knows the web address that authors can use to access the submission page for that specific article, and – once data has been submitted – that the journal and the author receive notice about the record identifier to include in print.

We’re happy to report that after several months of testing, this system is ready to roll out.  The first guinea pig for testing was The American Naturalist, which publishes a relatively small number of data papers.  Then Molecular Ecology, which publishes a whole lot more.  We are now in the process of setting up submission integration with a long list of partner journals, thanks to Tim Vines of Molecular Ecology, who has written an easy-to-follow instructions for the many journals that use the popular Manuscript Central software.

As a teaser for things to come, we are working to make data archiving even more like falling off of a log, by implementing one-stop data deposition, through Dryad, to one or more specialized repositories required by our partner journals.  Techniques like submission integration and handshaking should greatly facilitate submission to the repository and the usefulness of the data records.

For the curious, here’s a little more detail on how submission integration works. First, the journal automatically sends an email to Dryad upon acceptance of a manuscript. Dryad parses the incoming email and creates an (empty) record for each new article, with a unique identifier based upon the manuscript number.  Second, the author receives the link to the submission page for that article.  Since the bibliographic information about the paper is already stored in Dryad, all the author needs to do is follow the link, log in, and upload their datafiles. Not only does this save the author needless time re-entering author names, paper title and so on, but it also helps to ensure the information is accurate and properly formatted. Ideally, the author also provides a ReadMe document to promote reusability, and optional metadata to make the data more easily discoverable.  Third, upon submission, unique identifiers such as Handles or Digital Object Identifiers (DOIs) are assigned to the data. These identifiers can be resolved to web addresses.  The identifier for the whole record, or what we call the “data package”, is then included in the article according to the conventions of each journal, so that readers of the article can easily find the record in Dryad.   Most data packages will become available as soon as the issue comes out, although some may have an embargo of up to one year.  For more gory details, see our wiki pages.

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