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Archive for the ‘Data curation’ Category

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Dryad is thrilled to announce a strategic partnership with California Digital Library (CDL) to address researcher needs by leading an open, community-supported initiative in research data curation and publishing.

Dryad was founded 10 years ago with the mission of providing open, not-for-profit infrastructure for data underlying the scholarly literature, and the vision of promoting a world where research data is openly available and routinely re-used to create knowledge.

20,000 data publications later, that message has clearly resonated. The Dryad model of embedding data publication within journal workflows has proven highly effective, and combined with our data curation expertise, has made Dryad a name that is both known and trusted in the research community. But a lot has changed in the data publishing space since 2008, and Dryad needs to change with it.

Who/what is CDL?

CDL LoroCDL was founded by the University of California in 1997 to take advantage of emerging technologies that were transforming the way digital information was being published and accessed. Since then, in collaboration with the UC libraries and other partners, they have assembled one of the world’s leading digital research libraries and changed the ways that faculty, students, and researchers discover and access information.

CDL has long-standing interest and experience in research data management (RDM) and data publishing. CDL’s digital curation program, the University of California Curation Center (UC3), provides digital preservation, data curation, and data publishing services, and has a history of coordinating collaborative projects regionally, nationally, and internationally. It is baked into CDL’s strategic vision to build partnerships to better promote and make an impact in the library, open research, and data management spaces (e.g., DMPTool, HathiTrust).

Why a partnership?

CDL and Dryad have a shared mission of increasing the adoption and availability of open data. By joining forces, we can have a much bigger impact. This partnership is focused on combining CDL’s institutional relationships, expertise, and nimble technology with Dryad’s position in the researcher community, curation workflows, and publisher relationships. By working together, we plan to create global efficiencies and minimize needless duplication of effort across institutions, freeing up time and funds, and, in particular, allowing institutions with fewer resources to support research data publishing and ensure data remain open.

Our joint Dryad-CDL initiative will increase adoption of open data by meeting researchers where they already are. We will leverage the strengths of both organizations to offer new products and services and to build broad, sustainable, and productive approaches to data curation. We plan to move quickly to provide new value:

  • For researchers: We will launch a new, modern and easier-to-use platform. This will provide a higher level of service, and even more seamless integration into regular workflows than Dryad currently offers
  • For journals and publishers: We will offer new integration paths that will allow direct communication with manuscript processing systems, better reporting, and more comprehensive curation services
  • For academic institutions: We will work directly with institutions to craft right-sized offerings to meet your needs

We have many details to hammer out and a lot of work to do, but among our first steps will be to reach out to you — each of the groups above — to discuss your needs, wants, and preferred methods of supporting this effort. With your help, the partnership will help us grow Dryad as a globally-accessible, community-led, non-commercial, low-cost service that focus on breaking down silos between publishing, libraries, and research.

As this partnership is taking shape, we ask for community input on how our collective efforts can best meet the needs of researchers, publishers, and institutions. Please stay tuned for further announcements and information over the coming months. We hope you share our excitement as we step into Dryad’s next chapter.

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Alfred P. Sloan Foundation grant will fund implementation of shared staffing model across 7 academic libraries and Dryad

We’re thrilled to announce that Dryad will participate in a three-year, multi-institutional effort to launch the Data Curation Network. The implementation — led by the University of Minnesota Libraries and backed by a $526,438 grant from the Alfred P. Sloan Foundation — builds on previous work to better support researchers faced with a growing number of requirements to openly and ethically share their research data.

The result of many months of research and planning, the project brings together eight partners:

Currently, staff at each of these institutions provide their own data curation services. But because data curation requires a specialized skill set — spanning a wide variety of data types and discipline-specific data formats — institutions cannot reasonably expect to hire an expert in each area.

Curation workflow for the DCN

The intent of the Data Curation Network is to serve as a cross-institutional staffing model that seamlessly connects a network of expert data curators to local datasets and to supplement local curation expertise. The project aims to increase local capacity, strengthen cross-institutional collaboration, and ensure that researchers and institutions ethically and appropriately share data.

Lisa R. Johnston, Principal Investigator for the DCN and Director of the Data Repository for the University of Minnesota (DRUM), explains:

Functionally, the Data Curation Network will serve as the ‘human layer’ in a local data repository stack that provides expert services, incentives for collaboration, normalized curation practices, and professional development training for an emerging data curator community.

For our part, the Dryad curation team is excited to join a collegial network of professionals, to help develop shared procedures and understandings, and to learn from the partners’ experience and expertise (as they may learn from ours).

As an independent, non-profit repository, we are especially pleased to get to work more closely with the academic library community, and hope this project can provide a launchpad for future, international collaborations among organizations with similar missions but differing structures and funding models.

Watch this space for news as the project develops, and follow the DCN on Twitter: #DataCurationNetwork

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Dryad is a general purpose repository for data underlying scholarly publications. Each new submission we receive is reviewed by our curation team before the data are archived. Our main priority is to ensure compliance with Dryad’s Terms of Service, but we also strongly believe that curation activities add value to your data publication, since curated data are more likely to be FAIR (findable, accessible, interoperable, and reusable).

FAIR

Before we register a DOI, a member of our curation team will check each data package to ensure that the data files can be opened, that they appear to contain information associated with a scientific publication, and that metadata for the associated publication are technically correct. We prefer common, non-proprietary file types and thorough documentation, and we may reach out if we are unable to view files as provided.

Our curators are also on the lookout for sensitive information such as personally identifiable human subjects data or protected location information, and for files that contain copyright and license statements that are incompatible with our required CC0 waiver.

To make the data archiving process more straightforward for authors, our curation team has authored sets of guidelines that may be consulted when preparing a data submission for a public repository such as Dryad. We hope these guidelines will help you as you prepare your Dryad data package, and that they will lessen the amount of time from point of submission to registered data DOI!

A series of blog posts will highlight each of the guidelines we’ve created. First up is our best practices for sharing human subjects data in an open access repository, from former Dryad curator Rebecca Kameny.

— Erin Clary, Senior Curator – curator@datadryad.org

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Preparing human subject data for open access

Collecting, cleaning, managing, and analyzing your data is one thing, but what happens when you are ready to share your data with other researchers and the public?

peopleBecause our researchers come from fields that run the gamut of academia — from biology, ecology, and medicine, to engineering, agriculture, and sociology — and because almost any field can make use of data from human subjects, we’ve provided guidance for preparing such data for open access. We based our recommendations and requirements on well-respected national and international sources from government institutions, universities, and peer-reviewed publications.

Dryad curators will review data files for compliance with these recommendations, and may make suggestions to authors, however, authors who submit data to Dryad are ultimately responsible for ensuring that their data are properly anonymized and can be shared in a public repository.

handle-43946_960_720In a nutshell, Dryad does not allow any direct identifiers, but we do allow up to three indirect identifiers. Sound simple? It’s not. If the study involves a vulnerable population (such as children or indigenous people), if the number of participants is small, or if the data are sensitive (e.g., HIV status, drug use), three indirect identifiers may be too many. We evaluate each submission on a case-by-case basis.

If you have qualitative data, you’ll want to pay close attention to open-ended text, and may need to replace names with pseudonyms or redact identifiable text.

Quick tips for preparing human subjects data for sharing

  • Ensure that there are no direct identifiers.
  • Remove any nonessential identifying details.
  • Reduce the precision of a variable – e.g., remove day and month from date of birth; use county instead of city; add or subtract a randomly chosen number.
  • Aggregate variables that are potentially revealing, such as age.
  • Restrict the upper or lower ranges of a continuous variable to hide outliers by collapsing them into a single code.
  • Combine variables by merging data from two variables into a summary variable.

It’s also good research practice to provide clear documentation of your data in a README file. Your README should define your variables and allowable values, and can be used to alert users to any changes you made to the original dataset to protect participant identity.

Our guidelines expand upon the tips above, and link to some useful references that will provide further guidance to anyone who would like to share human subjects data safely.

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As the new year begins, we take note of the increasing diversity of fields represented in data archived at Dryad and review the numbers for 2016.

Dryad Grows into a General Repository

We are excited to see Dryad’s role in the preservation of data expand into new areas and fields in 2016. Researchers submitted more data involving human subjects and data from social media. In addition, a quick look at our most popular data shows that two of the top five downloaded packages were from the fields of cardiology and science journalism. While Dryad’s origins are in the life sciences, it is increasingly being used as a general repository for data from a myriad of fields.

Let’s take a look at the numbers for 2016:

Increase in Number of Data Packages and Data Files

Our curators were busy! The total number of published data packages (sets of data files associated with a publication) at the end of the year was a whopping 15,325. Our curators meticulously archived 4,307 packages, a 10% increase from 2015. The size of data packages also continued to grow – from an average of 481MB to an average of 573MB, an increase of about 20%.summary of Dryad data packages 2016

At the end of 2016, we were closing in on 50,000 archived data files; by January of this year, we passed that mark.

In a future blog, we’ll talk about the integration of new journals into the Dryad submission process, new members, and new partnerships. For now, we’ll just note that there was a 22% increase in the number of journals that have data in Dryad linking back to the article.

New Fields

We’ve seen a significant uptick in human subjects data and social media data this year, which has prompted us to develop an FAQ on cleaning and de-identification of human subjects data for public access. As the idea of what data should be preserved continues to broaden, submissions of these kinds of data will only increase. We’ll keep you updated about this trend in future blogs.

Top Downloads

Let’s take a look at the most popular data published in 2016, in terms of downloads. Among the top 5 downloads includes data on plant genetics, the early history of ray-finned fishes, and, not surprisingly in this age, the effects of climate change on boreal forests.

Also of interest are data from an article in Science evaluating how people make use of Sci-Hub, an open source scholarly library. Our guest blog on these data by science journalist John Bohannon generated a lot of interest this year and was one of our most popular blog posts ever.

Another significant development in 2016 came from the medical sciences. A comparison of coronary diagnostic techniques marked Dryad’s first submission from one of the top five cardiology journals, JACC: Cardiovascular Interventions.

The fact that 2 of the 5 top downloads come from fields outside of life sciences clearly indicates that data in Dryad now cover a broad range of fields.

Top 5 Downloads of Data Archived in 2016

Article Dryad DOI Number of Downloads
Wagner MR et al. (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications 7: 12151. http://doi.org/10.5061/dryad.g60r3 3123
Bohannon J et al. (2016) Who’s downloading pirated papers? Everyone.  Science 352(6285): 508-512. http://doi.org/10.5061/dryad.q447c 2969
D’Orangeville L et al. (2016) Northeastern North America as a potential refugium for boreal forests in a warming climate. Science 352(6292): 1452-1455. http://doi.org/10.5061/dryad.785cv 741
Johnson NP et al. (2016) Continuum of vasodilator stress from rest to contrast medium to adenosine hyperemia for fractional flow reserve assessment. JACC. Cardiovascular Interventions 9(8): 757-767. http://doi.org/10.5061/dryad.f76nv 453
Lu J et al. (2016) The oldest actinopterygian highlights the cryptic early history of the hyperdiverse ray-finned fishes. Current Biology 26(12): 1602–1608. http://doi.org/10.5061/dryad.t6j72 423

Overall, we’ve had a great year and are delighted to be seeing a broader range of data from an increasing number of journals and fields. Thanks to our Board of Directors, members, and of course our staff for providing their support to make 2016 a notable year for Dryad!

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Did you ever wonder what goes on behind the scenes when Dryad curators review data files submitted by authors?  There are no wizards behind our curtains, just real live information specialists and trained data curators.

by Kaptain Kobold via Flickr

by Kaptain Kobold via Flickr

Dryad’s curation process is intentionally lightweight, so it doesn’t delay the availability of the data. Curators don’t review the scientific merit of the files – that is left to peer reviewers and the scientific community. Instead, we rely on our curators’ expertise in library and information science to ensure the integrity and preservation of the data.

Curators perform basic checks on each submission (can the files be opened? are they free of copyright restrictions? do they appear to be free of sensitive data?). The completeness and correctness of the metadata is checked and the DOI is officially registered. During their work, Dryad curators encounter thousands of data files in any number of file formats. Our team examines all of these data files to ensure they do, in fact, include data, and not manuscripts, or pictures of kittens.

Curators may communicate directly with submitters to address issues and/or to make suggestions about enhancing the description and reusability of the data package. They can also create new versions of data packages should corrections or additions be needed after archiving. Ultimately, the responsibility for the content of the files rests with the submitters, but Dryad’s curators can help to catch and fix many common problems – and some rare ones, too.

fileTypes_wordleSince Dryad’s inception, curation operations have been led by the Metadata Research Center (or MRC) directed by Dr. Jane Greenberg, initially at the University of North Carolina at Chapel Hill, and now at Drexel University. The team is supervised by Senior Curator Erin Clary, and currently includes all students in, or graduates of, Library and Information Science (LIS) or Informatics Master’s programs.

So, (wizard) hats off to all our behind-the-curtains data curators, whose vital contributions ensure that the data in the repository is findable and usable. If you have a question about Dryad curation or need advice on preparing your data for archiving, don’t hesitate to email us at curator@datadryad.org.

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Dryad is a nonprofit organization fully committed to making scientific and medical research data permanently available to all researchers and educators free-of-charge without barriers to reuse.  For the past four years, we have engaged experts and consulted with our many stakeholders in order to develop a sustainability plan that will ensure Dryad’s content remains free to users indefinitely.  The resulting plan allows Dryad to recoup its operating costs in a way that recovers revenues fairly and in a scalable manner.  The plan includes revenue from submission fees, membership dues, grants and contributions.

A one-time submission fee will offset the actual costs of preserving data in Dryad.  The majority of costs are incurred at the time of submission when curators process new files, and long-term storage costs scale with each submission, so this transparent one-time charge ensures that resources scale with demand.  Dryad offers a variety of pricing plans for journals and other organizations such societies, funders and libraries to purchase discounted submission fees on behalf of their researchers.  For data packages not covered by a pricing plan, the researcher pays upon submission.  Waivers are provided to researchers from developing economies.  See Pricing Plans for a complete list of fees and payment options.  Submission fees will apply to all new submissions starting September 2013.

Membership dues will supplement submission fees, allowing Dryad to maintain its strong ties to the research community through its volunteer Board of Directors, Annual Membership Meetings, and  other outreach activities to researchers, educators and stakeholder organizations.  See Membership Information.

Grants will fund research, development and innovation.

Donations will support all of the above efforts.  In addition, Dryad will occasionally appeal to donors to fund special projects or specific needs, such as preservation of valuable legacy datasets and deposit waivers for researchers from developing economies.

We are grateful for all the input we have received into our sustainability plan, and look forward to your continued support in carrying out our nonprofit mission for many long years to come.

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