Open Science Resources

CZI Open Science Program

open science for biomedical research

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Publishing data with Dryad

Dryad is a digital repository for research data. The information below describes additional context useful for preparing and submitting biomedical data.

This 30 minute video includes an overview of material on this page, and is also available on our channel, with the slides available here.

Who publishes data in Dryad?

All research data is eligible for publication in Dryad. The main reasons researchers publish data in Dryad include:

Please view the complete list of Institutional and Publisher Members for more information.

If you are a CZI grantee and are not affiliated with a Dryad member organization, you can still publish data entries through Dryad at no cost through the CZI membership.

Benefits of publishing data in Dryad

Parts of a Dryad data entry

This section describes the general parts of a data entry, highlighting similarities and differences with publication in a journal, and identifying features that help your published data have the biggest impact.

Dryad maintains documentation about their submission process, which describes the steps in publishing an entry: uploading data, dataset curation, and dataset publication.

Data citation

An example of a typical Dryad entry is shown below (the original entry can be viewed here):

Example of a typical Dryad data entry

The information at the top of the page shows standard details that would be included in a citation of the data. This particular entry is associated with a journal publication, so the title is listed as “Data from:” followed by the title of the original article. In this case, the authors are identical to the published article (though as noted above, this is not a requirement). Additional information about the data publication is summarized under the Citation subheading.

The final section at the bottom of a Dryad data entry is Funding for the project. If you are a CZI grantee, please remember to acknowledge CZI as a funder, as this is important information for us to collect from among Dryad entries!

Abstract, methods, and data usage

The content below the citation can include a variety of information. If the data entry is from a publication, the Abstract is generally the same as the manuscript, though the abstract can be specific to the dataset as well. The following sections are Methods and Usage Notes, which describe how the data were collected/aggregated and information about using the data, respectively. One way to maximize the potential for data reuse is to include enough metadata in these sections such that the data can be understood and interpreted. For example, the schema (or data dictionary) for CORD-19 Software Mentions defines each of the columns in the dataset, so viewers can quickly understand what is represented in the data files:

Example of a Dryad entry with schema listed in Usage Notes

Data access

The Data Files box on the top right side of the page provides access to the data files. Clicking “Download dataset” saves a zip file of the entire set of files to your computer. The date(s) listed in the box represent a version of the data. (while most data entries have a single date listed, it is possible to provide updates to the data at a later point in time). clicking on the arrow next to the date reveals a list of the files in the dataset, which allows you to access each file individually. This is especially useful if the dataset contains many files, or files that are larger than average:

Example of files in a Dryad data entry

There are occassionally cases in which an author chooses to publish the data under an embargo: information about the data entry is published and visible, though the data files themselves cannot be viewed or downloaded until a specified date. The image below was taken prior to the October 27, 2021 publication data for this data entry, and demonstrates how an embargoed entry appears:

Example of an embargoed Dryad data entry

Additionally, a data entry can be submitted to Dryad under the “Private for Peer Review” feature. This means the dataset is kept private (not published publicly), although the files can still be shared with journals (reviewers and editors) and collaborators via a private URL.

Additional boxes on the right side include:

The Related Works box on the right side of the page include links to other websites relevant to the data. Often this is a single link which points to the published journal publication associated with the data, and is labeled as “Article”.

The following data entry features two additional categories for “Related Works”:

Example of preprint and software links

The final manuscript can be also listed as “Article” upon publication.

For data entries that are not formally linked to a single publication, the links may be listed as “Supplemental Information,” such as in this entry for the COVID Tracking Project.

Example Dryad data entries

The table below includes examples of Dryad data entries associated with biomedical research publications. These are shared to represent the breadth of data and file types published in Dryad.

Citation Data type
Russell, Alistair B.; Trapnell, Cole; Bloom, Jesse D. (2019), Data from: Extreme heterogeneity of influenza virus infection in single cells, Dryad, Dataset, annotated cell-gene matrix for the single-cell mRNA sequencing
Moffitt, Jeffrey R. et al. (2018), Data from: Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region, Dryad, Dataset, csv with measured properties of cells
Chauhan, Ganesh et al. (2019), Data from: Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting, Dryad, Dataset, methods, supplemental tables/figures, references
Hobson, Brad A. et al. (2019), Data from: TSPO PET Using [18F]PBR111 reveals persistent neuroinflammation following acute diisopropylfluorophosphate intoxication in the rat, Dryad, Dataset, MRI and positron emission tomography (PET) scans
Sampson, Timothy R. et al. (2017), Data from: Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease, Dryad, Dataset, xlsx files with motor function scores and cellular measurements
Gonzalez-Hunt, Claudia P. et al. (2015), Data from: Exposure to mitochondrial genotoxins and dopaminergic neurodegeneration in Caenorhabditis elegans, Dryad, Dataset, supplemental figures and tables
Nández, Ramiro et al. (2015), Data from: A role of OCRL in clathrin-coated pit fission and uncoating revealed by studies of Lowe syndrome cells, Dryad, Dataset, xlsx files of quantitative proteomics results
Schwarz, Niklas et al. (2019), Data from: Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease, Dryad, Dataset, images used to create 3D reconstructions, xlsx files with measurements of cells