Open data tips from the Dryad curation team | Part 1: Human subjects

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.

Dryad welcomes new board members

Today we celebrate our Board of Directors, and introduce three new members whose expertise and wide-ranging skills will help advance Dryad’s mission to provide free and easy access to data.

Dryad’s 12-member BOD supports and promotes our mission to make the data underlying scientific publications discoverable, freely reusable, and citable. The Board is comprised of diverse stakeholders, representing publishing, research, policy development, data networks, private funding, and scholarly organizations. BOD members are nominated by Dryad members and are elected or re-elected each year. They do not represent the organizations to which they belong; rather, they act as individuals in their involvement in the strategic planning and fiscal oversight of the company.

Who are the new members for 2017?

Adding to our esteemed Board of Directors this summer, we introduce our newest members:

Brian Hole (Class of 2020) will serve as treasurer of the Board. He is the CEO of Ubiquity Press, an open access publisher that focuses on alternative research outputs such as data, software, hardware, and bioresources. Previously, he managed the DryadUK project at the British Library, which focused on establishing a sustainable business model and publisher integrations, and also on building cost models for digital preservation. Brian brings a valued data-centric research background and detailed knowledge of open access publishing to Dryad this year.

 Fiona Murphy (Class of 2020) will serve as secretary of the Board. She is an independent research data and publishing consultant for institutions, societies, and commercial publishing companies and an Associate Fellow at the University of Reading. Fiona has written and presented widely on data publishing, open data, and open science. She has been involved in several research projects including PREPARDE, Data2Paper, and the Scholarly Commons Working Group. As an active member and sometime Co-Chair for several Research Data Alliance Groups focusing on data publishing policies, workflows, and accreditation systems, Fiona has organized several data-related events and sessions at scientific meetings.

Carly Strasser (Class of 2020) is a Program Officer at the Gordon and Betty Moore Foundation and is especially interested in open science and scholarly communication. She works in the Data-Driven Discovery Initiative, which is focused on promoting both the researchers and the practices required for high impact data-driven research. Previously, Carly was a Research Data Specialist at the California Digital Library where she was involved in development and implementation of many of the University of California Curation Center’s services, and worked to promote data sharing and good data management practices. Carly’s prior experience as a researcher in marine science and mathematical ecology has informed her work of ushering in the new era of open, transparent, and collaborative science.

We wish to thank our current and past members for bringing their expertise and passion to help advance Dryad’s mission and we look forward to their contributions and to another exciting year of open data.

Sharing the wealth: Data re-use with ultrahigh resolution MRI data

We present a guest post from researcher Falk Lüsebrink highlighting the benefits of data sharing. Falk is currently working on his PhD in the Department of Biomedical Magnetic Resonance at the Otto-von-Guericke University in Magdeburg, Germany. Here, he talks about his experience of sharing early MRI data and the unexpected impact that it is having on the research community.

Early release of data

The first time I faced a decision about publishing my own data was while writing a grant proposal. One of our proposed objectives was to acquire ultrahigh resolution brain images in vivo, making use of an innovative development: a combination of an MR scanner with ultrahigh field strength and a motion correction setup to remediate subject motion during data acquisition. While waiting for the funding decision, I simply could not resist acquiring a first dataset. We scanned a highly experienced subject for several hours, allowing us to acquire in vivo images of the brain with a resolution far beyond anything achieved thus far.

 MRI data showing the cerebellum in vivo

MRI data showing the cerebellum in vivo at (a) neuroscientific standard resolution of 1 mm, (b) our highest achieved resolution of 250 µm, and (c) state-of-the-art 500 µm resolution.

When our colleagues saw the initial results, they encouraged us to share the data as soon as possible. Through Scientific Data and Dryad, we were able to do just that. The combination of a peer-reviewed open access journal and an open access digital repository for the data was perfect for presenting our initial results.

17,000 downloads and more

‘Sharing the wealth’ seems to have been the right decision; in the three months since we published our data, there has been an enormous amount of activity:

A distinct need for data re-use

MRI studies are highly interdisciplinary, opening up numerous opportunities for sharing and re-using data. For example, our data might be used to build MR brain atlases and illustrate brain structures in much greater detail, or even for the first time. This could advance our understanding of brain functions. Algorithms used to quantify brain structures needed in the research of neurodegenerative disorders could be enhanced, increasing accuracy and reproducibility. Furthermore, by making available raw signals measured by the MR scanner, image reconstruction methods could be used to refine image quality or reduce the time it takes to collect the data.

There are also opportunities beyond those that our particular dataset offers. A recent emerging trend in MRI comes from the field of machine learning. Neuronal networks are being built to perform and potentially improve all kinds of tasks, from image reconstruction, to image processing, and even diagnostics. To train such networks, huge amounts of data are necessary; these data could come from repositories open to the public. Such re-use of MRI data by researchers in other disciplines is having a strong impact on the advancement of science. By publicly sharing our data, we are allowing others to pursue new and exciting directions.

Download the data for yourself and see what you can do with it. In the meantime, I am still eagerly awaiting the acceptance of the grant application . . . but that’s a different story.

The data: http://dx.doi.org/10.5061/dryad.38s74

The article: http://dx.doi.org/10.1038/sdata.2017.32

— Falk Lüsebrink

And Now, the Numbers . . .

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!

Researcher Profile: Zach Gompert

We’re beginning a series highlighting researchers who use Dryad to openly publish their research data. We ask them about their current projects, why they believe in open science, and why they choose Dryad.

photo of Zach Gompert

Zach Gompert

For our first researcher profile, we talked with Dr. Zach Gompert, assistant professor in the Department of Biology at Utah State University, about how his work ties in with open science:

Dryad: What is your area of research and what’s your current focus?

Gompert: The overarching goal in my lab is to advance understanding of the extent, organization, causes, and consequences of variation in nature. Some of the issues were are investigating are:

  • What are the evolutionary consequences of hybridization?
  • How does the evolution of novel ecological interactions affect biodiversity?
  • Is temporal variation in natural selection a key determinant of genetic diversity levels in natural populations?

We address these questions through population genomic analyses of natural and experimental populations, and through development of new theory and statistical methods. Our work on Lycaenid butterflies shows that hybridization can be a key creative force in animal evolution and that evolutionary histories are not always well represented by the ‘evolutionary tree’ metaphor. In other words, lineages don’t just split, they come back together.

We have quite a few datasets in Dryad now, including partial genome sequences from over a thousand butterflies.

butterfly in field

Lycaeides melissa

Dryad: What do you think about open science in general? What are advantages of open science? 

Gompert: Science has always been a communal endeavor. Large-scale collaboration is vital now for a number of reasons:

  • Diverse expertise. Many key questions require a diverse group of investigators. This results in big, multifaceted datasets and necessitates rapid sharing of data, methods, and findings.
  • Re-purposing data. It’s common now for data and methods to have applications beyond those that they were originally collected or developed for. Open science allows these to be used by other investigators, accelerating the rate of discovery.
  • Data integrity. Openness ensures a higher level of quality and integrity. When data and methods are available for scrutiny, possible errors are more likely to be identified and corrected. This is particularly relevant for large-scale, multi-investigator projects.
  • Public funding and access. Since much of science is funded by the public, I think scientists have an ethical duty to make the products of research available to everyone.

Dryad: In your opinion, what are disadvantages or concerns about open science?

Gompert: There are two common concerns:

  • Getting scooped. Researchers can be scooped if another group analyzes and publishes the data they generated. While this has some validity, sufficient safeguards and community standards are in place to minimize this problem, and it’s minor compared to the advantages of openness.
  • Poor documentation. I think data archiving is in better shape than it once was, but much of archived data or code are not sufficiently documented to truly be useful to others. Enhancing documentation of data is a big area where we as a community need to do more.

Dryad: You have over 20 datasets archived in Dryad. What do you see as the benefits of data sharing in Dryad?

Gompert: The primary strength of Dryad is its flexibility, specifically the ability to archive diverse types of data (and computer code) in a single location and to link to other more specialized databases such as NCBI. With Dryad, researchers have a central location where they can find all of the data associated with a publication.