Frequently Asked Questions

Frequently Asked Questions 

Submitting data 

Why use Dryad?

Dryad aims to make data archiving as simple and as rewarding as possible through a suite of services not necessarily provided by publishers or institutional websites:

Simple

  • Dryad welcomes data files associated with any published article in the sciences or medicine, as well as software scripts and other files important to the article.
  • There is no restriction regarding data formats.
  • Dryad works with journals to integrate article and data submission, streamlining the submission process. Once the files are prepared, submission typically takes less than 15 minutes.
  • Dryad provides a single clear and best-practice option for terms of reuse.
  • A curator will check your files for technical problems before they are released.
  • By default, data are embargoed until journal article publication. Dryad makes sure this happens so you do not need to.
  • If it is supported by the policy of the journal, you may, during the submission process, select a ‘no-questions-asked’ embargo on data downloads for one year post-publication. Dryad will support a longer embargo if directed by a journal editor.
  • You are free to provide additional keywords that make the data easier to discover and additional documentation (in the form of ReadMe files) to help ensure proper data reuse.
  • You have the ability to add new versions of data files in order to make updates or corrections.
  • Dryad can make data securely available for peer review if the manuscript has been submitted to a participating partner journal.

Rewarding

  • Dryad works to ensure that you get credit for reuse of your data by promoting data citation and the tracking of data reuse.
  • Data files receive persistent, resolvable Digital Object Identifiers (DOIs) that can be used in a citation as well as listed on your CV.
  • Dryad’s open terms of reuse facilitate the maximum impact for your work.
  • Data in Dryad can be discovered independently of the publication, providing a new route by which others may learn about your work.
  • Dryad provides open metadata in order to enable discovery of your data through third party services.
  • Usage statistics are available for you to highlight when your datasets are frequently downloaded.
  • Since Dryad does not reject data for being of the wrong type or in the wrong format, all the orphan data files associated with an article can be archived together.
  • Dryad can host files that are larger than those accepted by most journal websites (ordinarily up to 10 GB per package).
  • Dryad is a nonprofit that is committed to its mission of making data available for research and educational reuse for now and into the future.
  • Your data is preserved and will be available for the long-term, through participation in the DataONE network.
  • Dryad is responsive to the needs of the research and education community through its community of users and members.
  • Dryad is a participant in organizations such as BioSharing, DataCite and DataONE. You as a researcher benefit from, and contribute to, the work of these organizations by submitting to and using Dryad.

What is Submission Integration?

See Journal Integration

What kinds of data does Dryad accept?

Dryad hosts research data underlying scientific and medical publications. Historically, the repository has been strongest in the life sciences. Most data in the repository is associated with peer-reviewed journal articles, but data associated with non-peer reviewed publications from other reputable sources (such as dissertations and books) is also accepted. At this time, all descriptive information must be in English.

Most types of files can be submitted (e.g., text, spreadsheets, video, photographs, software code) including compressed archives of multiple files. View additional guidance on preservation-friendly file types.

Ordinarily, no more than 10GB of material are submitted for a single publication; larger data sets are accepted subject to additional charges.

Data that was originally collected for another publication may be submitted as long as it is referenced by the current publication. Non-data files may also be submitted to Dryad provided the files are integral to the publication and can be released to the public domain. Note that policies for the whether to submit non-data Supplementary Materials to the journal or to Dryad vary among journals.

Dryad does not accept submissions that contain personally identifiable human subject information since all data is publicly available. Human subject data must be properly anonymized and prepared under applicable legal and ethical guidelines. The following article may be helpful: Hrynaszkiewicz I, Norton ML, Vickers AJ, Altman DG (2010) Preparing raw clinical data for publication: guidance for journal editors, authors, and peer reviewers. BMJ 340, c181. http://dx.doi.org/10.1136/bmj.c181

Dryad does not accept any files with licensing terms that are incompatible with the Creative Commons Zero waiver.

While Dryad can host software scripts and snapshots of software source code, we recommend the use of a public software repository with version control for the ongoing maintenance of software packages. Software in Dryad must be released with a Creative Commons Zero waiver.

In what file format(s) should I submit my data?

Due to the diversity of datatypes hosted by the repository, Dryad does not require a single file format, or even set of file formats, but rather encourages users to follow accepted community standards where they exist. Users are strongly encouraged to ensure that data can be easily extracted from the files provided (e.g., by using CSV rather than PDF). View additional guidance and a list of preservation-friendly file formats.

When should I submit my data?

Your data may be submitted at various points in the publication process. Journals that are integrated with Dryad have specific requirements.

  • If you received an invitation to submit data to Dryad from a journal, then that journal has integrated its submission process with Dryad. Please follow the instructions from the journal to determine whether the data should be submitted before review (at the time of initial manuscript submission) or upon acceptance (but still prior to publication).
  • Some integrated journals prefer (or require) authors to begin their data submission before submitting their manuscript, and to include their Dryad DOI as part of their manuscript submission.
  • If the data accompany an article in a journal that has not integrated its submission process (i.e., not on our list of integrated journals) the best time to do so is immediately after you receive notice of acceptance.
  • You may also submit data associated with previously published works, in which case you can simplify the submission process by entering the DOI or PubMedID to get started.
  • If a delayed-release data embargo is allowed by your journal, you may select that option at the time of submission, prior to publication.

Dryad Submission Process

How can I modify files I have submitted to Dryad while my article is in review?

Some integrated journals enable their authors to make data privately available to editors and reviewers, during the article review process.  Dryad does not allow files to be deleted while an article is under review. We only allow additions during this time. This restriction ensures that all reviewers see the files that were originally submitted.

To add corrected files, log into your Dryad account and click on the "My Submissions" link in the menu. Select the appropriate data package. At the bottom of the page for this package, you will see a button "Add new data file". After you have finished adding data files, please email help@datadryad.org to indicate which files should be retained during the final curation process.

Once your article has been accepted for publication, the Dryad curators will remove duplicate or superseded files. If the manuscript is rejected, the files remain in your review workspace, and may be associated with another journal.

What should I prepare before submission?

Providing well-documented data in a community-accepted format is in the interest of the submitter since it encourages others to reuse and thus cite the original work. It is the shared responsibility of the submitter, the editors, and the reviewers to ensure the data are provided according to community standards. In some cases, journals provide explicit guidelines in their instructions to authors. In the absence of such guidance, the BioSharing registry may be helpful in identifying applicable data exchange formats where they exist.

For general guidance on how to prepare data for submission, submitters may wish to consult DataONE and the following publication: White EP, Baldridge E, Brym ZT, Locey KJ, McGlinn DJ, Supp SR (2013) Nine simple ways to make it easier to (re)use your data. Ideas in Ecology & Evolution 6(2):1–10. http://doi.org/10.4033/iee.2013.6b.6.f

Submitters should aim to provide sufficient data and descriptive information such that another researcher would be able to evaluate the findings described in the publication. This will generally include any data that are used in statistical tests, as well the individual data points behind published figures and tables.

Submitters are advised to follow community data standards for the content and format of data files where applicable, to avoid proprietary and binary file formats where possible, and to ensure that data can be easily extracted from the files provided (e.g., by using CSV rather than PDF). View additional guidance on preservation-friendly file formats.

We strongly encourage submitters to include one or more ReadMe files that provide additional information to help users make sense of the files (e.g., instructions for use with software scripts, variable abbreviations, measurement units, and data codes). View additional guidance on ReadMe files.

How can I make my data submission as accessible and reusable as possible?

  • Submit your data files in non-proprietary formats from which data can be easily extracted (e.g., CSV rather than PDF).
  • Consider submitting your data files in multiple formats if you think that will enhance their ability to be reanalyzed. View additional guidance and a list preferred Dryad file formats.
  • Provide descriptive information within your data files (e.g., column headers in a spreadsheet).
  • Provide a ReadMe file that provides contextual information about the data file so that it can be interpreted correctly.
  • Provide titles, descriptions and keywords for your datafiles, to make the data more discoverable and to assist in understanding the relationship of the datafile to the publication.

How do I submit data?

The submission process is designed to be self-explanatory, but here is what you can expect:

  • You will need to register the first time you come to Dryad and be signed in so that you can return to a submission at a later date should it be necessary.
  • If you received a customized Dryad submission URL from your journal, please use that to enter the system so that the manuscript information can be automatically retrieved.
  • If you are entering data for a previously published work, you may use a DOI or PubMedID to pull up the publication information.
  • If the prior publication lacks a DOI and PubMedID, or if you are submitting data prior to publication in a journal that is not yet integrated with Dryad, you will first need to describe the publication (e.g. the author names, the title, the journal).
  • You will need to make a legal affirmation on behalf of all the authors that the data can be released under a CC0 license.
  • Then you will upload your data files and ReadMe files and modify the metadata to your liking. You have the opportunity to save an incomplete submission and return to it later.

If you encounter any difficulties, or realize that you need to make modifications after you have submitted your data package, please contact us through our web form or email help@datadryad.org.

How do I write a ReadMe file?

A ReadMe file is intended to help ensure that the data can be correctly interpreted. You may submit one ReadMe for the data package as a whole and/or provide a separate ReadMe for each individual data file to supplement the file descriptions. We recommend that a ReadMe be a plain text file containing the following:

  • for each filename, a short description of what data it includes
  • for tabular data: definitions of column headings and row labels; data codes (including missing data); and measurement units
  • any data processing steps, especially if not described in the publication, that may affect interpretation of results
  • a description of what associated datasets are stored elsewhere, if applicable
  • whom to contact with questions

View additional guidance on ReadMe files.

How do I cite the data in my manuscript?

Data citation practices are actively evolving and vary among journals. Dryad does not have a recommendation for the placement of data citations at this time. Some publishing organizations, such as CrossRef, recommend reporting the data both in the text (e.g., within the Methods or in a dedicated Data Availability section) and in the Bibliography.

When referencing data in the text, we recommend the following as a template:

Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.[NNNN]

In the Bibliography, we recommend a citation similar to:

Heneghan C, Thompson M, Billingsley M, Cohen, D (2011) Data from: Medical-device recalls in the UK and the device-regulation process: retrospective review of safety notices and alerts. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.585t4

Do I have the option to embargo release of my data?

By default, data are released at the time the publication is made available online. Some journals that have integrated their submission process with Dryad allow authors to designate that individual files be released one year after the date the publication is made available online. The embargo option can be selected within the Dryad interface at the time of data submission. Longer embargoes can be granted only with written permission from the journal editor or publisher. If selected, the metadata for the file will be visible on the publication release date, but the file itself will not be downloadable until the embargo expires.

Embargoing the data prior to publication guarantees that the data are safely archived, but not accessible, while the original authors complete ongoing work. However, we encourage researchers to use this option sparingly; the risk of being scooped on a forthcoming publication is generally quite small, while a negative citation impact from delaying the release of the data is likely to be widespread. Note also that only the data required to support the claims made in the publication need to be archived. Of course, you are welcome to archive more if you like.

How much does it cost?

Since a guiding principle of Dryad is to make its contents freely available for research and educational use, there are no access costs for individual users or institutions. Instead, Dryad supports its nonprofit mission by recovering costs up front.

Dryad collects a Data Publishing Charge (DPC) upon publication. The submitter is asked to commit to this charge at the time of submission, and is charged if the accompanying publication is accepted, unless

  1. the associated journal, or another organization, has already contracted with Dryad to cover the DPC, or
  2. the submitter is based in a country classified by the World Bank as a low-income or lower-middle-income economy.

To determine whether your DPC will be covered, look up your journal. If there is no payment plan or sponsor in place, the DPC is $90. At this time, we are only able to accept credit cards in payment for DPCs (personal or institutional cards). We regret that we are currently unable to issue invoices for individual submissions.

Additional charges will apply to data packages in excess of 10 GB and from journals without integrated submission. The price schedule is detailed here.

What happens to data after it is submitted?

Dryad performs basic checks on each submission (can the files be opened? are they free of viruses? are they free of copyright restrictions? do they appear to be free of sensitive data?). The completeness and correctness of the metadata (e.g. information about the associated publication, the date on which any embargo is to be lifted, indexing keywords) are checked and the DOI is officially registered.

The data packages are discoverable and backed up for long-term preservation within the DataONE network. The information content of the original file is never intentionally modified or processed, but copies may be made in different file formats to facilitate preservation.

The data package is publicly released once the online version of the associated publication is available (unless an alternative release option has been selected), and the metadata are shared with indexing services to promote discoverability.

Can I see how often my data package is being viewed and downloaded?

Yes, Dryad counts data package views and data file views and downloads, and displays this information on each data package and data file page. While considerable effort has been made to exclude automated web crawlers from Dryad’s counts, views and downloads may still be overestimates of human usage.

You may also monitor the impact of Dryad data packages and files through citations, sharing links on social media, etc. using emerging services such as ImpactStory.org, altmetric.com and the Data Citation Index. While some of these services do allow you to see who has discussed your data on social media, Dryad does not track, and cannot report, the identity of the individuals who view or download files.

Using data 

How may data from Dryad be reused?

The data hosted by Dryad have been dedicated to the public domain, to the extent possible under the law, under the terms of Creative Commons Zero (CC0), in order to minimize legal barriers and maximize the impact on research and education. However, CC0 does not waive other persons’ rights in the work (e.g., privacy) and, in many jurisdictions, does not waive your moral rights as an author (e.g., to the integrity of the work). Furthermore, while CC0 does not assert a legal requirement for attribution, community norms for scholarly communication do set expectations for how to attribute the original creators. Some partner journals provide authors the option of a limited-duration embargo (typically one year) from the time of publication before the data become available, and journal editors have the discretion to grant longer embargoes under special circumstances.

Note that a very small number of early submissions to Dryad are available under a license other than CC0.

Do I have to pay to download or use the data?

No, all the content in Dryad is free to download and reuse.

How do I cite data from Dryad?

When citing data found in Dryad, please cite both the original article as well as the Dryad data package. It is recommended that the data package be cited in the bibliography of the original publication so that the link between the publication and data is indexed by third party services. Dryad provides a generic citation string that includes authors, year, title, repository name and the Digital Object Identifier (DOI) of the data package, e.g.

Westbrook JW, Kitajima K, Burleigh JG, Kress WJ, Erickson DL, Wright SJ (2011) Data from: What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8525

Dryad also assigns a DOI to each data file, which should only be used in contexts where the citation to the data package as a whole is already understood or would not be necessary (such as when referring to the specific file used as part of the methods section of an article).

If you are using a large number of data sources, it may be necessary to provide a list of the relevant data packages/files rather than citing each individually in the References. The list can then be submitted to Dryad so others who read your publication can locate all of the original data.

How can I download information to my citation management software?

Data citations can be easily downloaded using the links at the bottom of the Citation Box on the data package page. Citation can currently be downloaded in two generic formats: RIS (compatible with software such as EndNote, Reference Manager, ProCite, and RefWorks) and BibTex (compatible with software such as LaTeX and BibDesk)

You may also use links in the Citation Box to bookmark or share a link to the data package on a variety of platforms (e.g. Delicious, Facebook, Twitter and Reddit).

General information 

What is a data package?

A data package is the entire set of data files associated with one publication plus the metadata describing the combined set.

Does my journal work with Dryad, and how?

Journals may work with Dryad in a number of ways. First, a journal may have integrated its submission process with Dryad. The journal may choose a number of options, e.g. directing authors to submit data either before review or after acceptance and whether to allow data embargoes or not. Second, journals or their parent organizations may handle Data Publishing Charges on behalf of authors. Third, journals and their parent organizations may participate in Dryad’s governance through Membership. To see what relationship, if any, your journal has to Dryad, please consult this Table. We welcome inquiries from journals not yet listed, and encourage authors to suggest Dryad as a data archiving service to their editors.

What is a Dryad DOI?

Each data package and data file in Dryad is assigned a Digital Object Identifier, or DOI, a permanent, globally unique, and resolvable identifier that is an important component of a data citation.

We recommend using the URL form of the DOI (e.g. “http://dx.doi.org/10.5061/dryad.6h722”) whenever referencing a data package or data file.

The DOI for each data file is composed of the base DOI for the data package “http://dx.doi.org/10.5061/dryad.[NNNN]” with the version number appended as “/1″, “/2″, etc. When a new version of a data package or data file are released, the DOI is updated with the suffix “.2″, “.3”, etc. Thus the third version of the second data file in the second version of a Dryad data package would have a DOI of the form http://dx.doi.org/10.5061/dryad.[NNNN].2/2.3. Note that the DOI without the version suffix will resolve to the most recent version, and the presence of older versions will be indicated.

Dryad DOIs are assigned through the EZID service from the California Digital Library and are registered by DataCite.

Why does Dryad use Creative Commons Zero?

CC ZERO

All data submitted to Dryad is released to the public domain under Creative Commons Zero (CC0), which reduces legal and technical impediments to the reuse of data by waiving copyright and related rights to the extent permitted by law. In most cases, CC0 does not actually affect the legal status of your data, since facts in and of themselves are not eligible for copyright in most countries (e.g. see this commentary from Bitlaw regarding U.S. copyright law).

CC0 does not exempt those who reuse the data from following community norms for scholarly communication, in particular from citation of the original data authors. On the contrary, by removing unenforceable legal barriers, CC0 facilitates the discovery, reuse, and citation of that data. Any publication that makes substantive reuse of the data is expected to cite both the data package and the original publication from which it was derived.

"Community norms can be a much more effective way of encouraging positive behaviour, such as citation, than applying licenses. A well functioning community supports its members in their application of norms, whereas licenses can only be enforced through court action and thus invite people to ignore them when they are confident that this is unlikely." (Panton Principles FAQ)

"…when you federate a query from 50,000 databases (not now, perhaps, but definitely within the 70-year duration of copyright!) will you be liable to a lawsuit if you don’t formally attribute all 50,000 owners?" (Science Commons Database Protocol FAQ)

Similarly, we do not support the use of licenses that (questionably) assert copyright and add well-meaning, but potentially problematic, restrictions on reuse, such as “non-commercial”, “no derivative” and "share-alike" conditions.

"... given the potential for significantly negative unintended consequences of using copyright, the size of the public domain, and the power of norms inside science, we believe that copyright licenses and contractual restrictions are simply the wrong tool [for data], even if those licenses and contracts are used with the best of intentions." (Science Commons Database Protocol FAQ)

Dryad’s use of CC0 to make the terms of reuse explicit has some important advantages:

  • Interoperability: Since CC0 is both human and machine-readable, other people and indexing services will automatically be able to determine the terms of use.
  • Universality: CC0 is a single mechanism that is both global and universal, covering all data and all countries. It is also widely recognized.
  • Simplicity: There is no need for humans to make, or respond to, individual data requests, and no need for click-through agreements. This allows more scientists to spend their time doing science.

It is important to note that if you have data that, due to pre-existing agreements, cannot be released under the terms of CC0, please do not submit that data to Dryad. Journals that require data archiving as a condition of publication can make exceptions for such special cases.

How are data packages in Dryad backed up?

Data packages in Dryad are replicated across multiple systems to support failover, improve access times, allow recovery from disk failures, and preserve bit integrity. The data packages are discoverable and backed up for long-term preservation within the DataONE network.

Dryad's content is not currently being replicated through the CLOCKSS digital library network. A CLOCKSS working group is developing a new and separate set of guidelines for databases; when these are in place, it may be possible for Dryad to enter into a new agreement with CLOCKSS.

Can the Dryad repository help me prepare a data management plan?

Yes, we encourage researchers to include Dryad as part of their data management plan when applying for grants or developing a data management strategy for their institution. Data submitted to Dryad can help researchers meet expectations (e.g. for funders in the US and UK) that data be archived for long-term preservation, available for reuse at no cost and with open, explicit terms of reuse. We recommend consulting an online data management planning tool such as DMPTool or DMPOnline.

What are the charges for submitting data?

See Pricing Plans and Data Publishing Charges

What journals are integrated with Dryad?

See Integrated Journal Table

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Last revised: 2014-08-27