Templates for Correspondence

The following templates are used as a basis for common curator and other staff correspondence with depositors and journal editors.

Cannot invoice individuals
We regret that Dryad is unable to issue an invoice for individual submissions. We only offer invoicing for our payment plans. If your institution would like to sponsor multiple submissions to Dryad, we would be happy to establish a payment plan to accomplish this. Many journals also sponsor submissions to Dryad on behalf of their authors.

When there is no payment plan or sponsor in place, we request that you enter a valid credit card number. You may use your personal card or an institutional card (if permitted by the institution). The card will not be charged until your data has been accepted by our curators and its associated article (or other publication) has been accepted for publication, is in press or has already been published. When the card is charged, you will receive a receipt via email.

We look forward to receiving your submission.

Submissions kicked to the "Reauthorize Payment" queue
Subject: Your recent submission to Dryad Digital Repository

Thank you for your recent submission of data associated with "Article title."

Our system was unable to authorize your credit card payment. Please log in to Dryad and navigate to https://datadryad.org/submissions to reenter payment information. As soon as we receive payment, we will finish processing your submission.

Please contact us at help@datadryad.org if you have additional questions. Thanks for choosing to archive and share your data!

Waivers only provided to authors in developing countries
At this time, Dryad only grants waivers to researchers based in economically developing countries (there is a list in the submission system). I regret that we cannot offer you a waiver.

More than 40 journals currently sponsor deposits in Dryad so that authors do not have to pay (see the list at https://www.datadryad.org/pages/integratedJournals).

We hope [Journal Name] will consider becoming a sponsor.

Permanence and stability of the repository
We take our commitment to the long-term preservation of data seriously. Dryad’s infrastructure is designed with multiple layers of protection, and is continually being improved to keep up with best practices in digital archiving.

Preserving the Bits

Repository contents are incrementally backed up every ten minutes. Full backups are made every 24 hours.

The repository is mirrored with sites in the United States (at the North Carolina State University Digital Library) and in the United Kingdom (at the British Library); we aim to have additional service mirrors in the future. We are proud that, to date, the service has had 99.7% uptime.

To provide further redundancy, Dryad is a member node within the DataONE data preservation network, and is expecting to become a member of CLOCKSS. Should Dryad cease operations at some point in the future, all existing content would still be available from one of these networks.

Dryad assigns DOIs to data packages and files, which helps ensure that users will still be able to find the content online for many years to come.

Preserving the Contents

To guard against digital file format obsolescence, Dryad is implementing curation processes, such as conversion of commonly used proprietary or binary formats to “preservation formats,” and periodic migration of files from old to new formats. At the same time, the files provided by the depositor will remain available in their original format.

Dryad uses highly portable technology. The software platform is built upon DSpace, sophisticated open-source software platform for managing digital collections, used by hundreds of institutions around the world, and actively maintained by DuraSpace, a non-profit foundation dedicated to "open technologies for durable digital content."

Preserving the Organization

In addition to the technical infrastructure, Dryad’s governance and business model are designed to provide for long-term organizational stability.

Dryad is in the process of incorporating as a not-for-profit organization overseen by a membership-elected board. Members of Dryad include a robust network of stakeholders with a strong interest in seeing the repository persist, including journals, scientific societies, publishers, and other institutions.

Dryad has a sustainability plan and business model which ensure that revenues from payments for the submission of new data deposits cover the repository’s operating costs (including curation, storage, and maintenance). Thus, long-term funding for Dryad is not dependent on a small number of grants, or the continued largesse of a single host institution.

What is a data file?
Data is the raw information that is analyzed in a scientific article. At Dryad, we call each file (e.g. an excel spreadsheet, a text file, etc) a "data file" to help differentiate between the files themselves and the "data package," which can include multiple files. For example, this data package: http://datadryad.org/resource/doi:10.5061/dryad.8837q is made up of three data files: Sample&EcologicalData.xlsx, GeneticData.xlsx, and MorphologicalData.xlsx. Dryad doesn't want the written article -- that will be published in the journal. [Optional: Your article abstract states... guess what data they might want to archive]

Manuscript numbers: "short" vs. "extended"
Dr. XXXX,

Journal XXX uses "extended" manuscript numbers for entries in Dryad. This means that instead of your normal manuscript number of XXXXX, you must also include your user ID number, like this: XXXXX

You can log into Dryad and enter the extended number above to access your information, or you can click on this URL: XXXXXXX

Sorry for the confusion. Dryad serves a broad range of journals, and they do not all use the same systems for identifying submissions to Dryad. We are working on ways to make our submission system more intuitive for submitters from all journals.

Account creation and log in problems
Need account to submit data

You must have a Dryad account and be logged in to submit data. Creating an account allows us to communicate with you about the status of your submission(s), and gives you a personal workspace where you can access and manage your data packages during certain stages of the archiving process. You may sign up for a new account or log in at https://datadryad.org/password-login.

Please let us know if you have any further questions about the submission process. You may find our FAQ page helpful as you get started: http://datadryad.org/pages/faq

Verification emails from the registration system

If someone complains that they didn't receive a verification email, first check whether they have already registered for a Dryad account. (In your admin menu, choose Access Control-->People, and then search for the email address.) When someone attempts to re-register with the same email address, no error message is displayed, but the system fails to send a verification email.

If they are already registered:

There is already a Dryad account associated with this email address. Try logging in, using the forgotten password link if needed: .

If they are not already registered:

I just tested the registration system, and it generated an email correctly, so the problem is somewhere in between the email being sent and it showing up in your inbox. Have you checked your spam folder? The sending address will be help@datadryad.org and the subject line will be "Dryad Account Registration." Let us know if that doesn't do the trick.

Problems submitting -- depositor didn't log in

I tested your manuscript number, and the Dryad submission system recognizes it. The most likely problem is that you simply need to create a Dryad account and log in. You can do this by clicking the link the journal sent you, or going directly to the log in page here:

http://datadryad.org/login

Thanks and let us know if your have any further trouble.

Email address associated with account needs to be changed
Thank you for alerting us to your email address change. We hope to add functionality that will allow users to update this themselves, but for now we must make the change for you.

I have updated the address associated with your Dryad account to ________ -- please use this to log in from now on.

You may find that you can longer see your previously-archived items under "My Submissions" (https://datadryad.org/submissions). Please let us know if you would like this access restored.

Instructions to modify and resubmit a data package
To access and update your data package:

-Please log in at http://datadryad.org/password-login -Click on the title of your data package under ‘unfinished submissions’ -You may need to click “resume” at the bottom of the next page, and then save your publication details. -At the ‘submission overview’ screen, you can modify your existing data files by clicking “verify” next to the file. At the next screen, click “remove” to delete the existing file, and then browse to the modified version on your server. -You may also upload new files using the “add new data file” button. -When you have finished, you are welcome to finalize and resubmit your data package.

-PLEASE NOTE: if any file says “verify” next to it, you must click on this button and at the bottom of the next screen click ‘save file and continue’. This must be done before the button to “continue to checkout” will appear.

No "finalize & submit" / checkout button
It sounds as though you need to verify and save all of your individual data files/metadata. Any file that says "verify" next to it must be saved before you can submit.

Please click the "verify" button next to one file. At the next screen, if your file is uploaded and the metadata looks okay, then at the bottom of the page, please press "save file and continue". It may take a moment, but the system should lead back out to the submission overview page (where all of your files are listed), and the "verify" button should be replaced by one that says "edit".

Once all files are confirmed completed, you should see the button to 'continue to checkout'.

Modifying a submission in Journal Review
The actions you can perform while a submission is in review are limited. 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.

___

[when user has emailed]:

Thank you for clarifying the contents of your data submission. "[filename]" has been marked as superseded and will be removed from your data package when it is processed by our curators.

Please let us know if anything else comes up, and thanks for supporting open data and Dryad.

Payment questions/receipt requests while submissions are still in review
Thanks for contacting us. Your data submission is still "in review," meaning that you have not yet been charged for it. If you were asked to enter a credit card number, your card has been verified, but will be not be charged until the associated article is accepted and our curatorial team approves your submission. This ensures that users are never charged for submissions that may not end up being archived.

You will receive a confirmation and a receipt when your card is charged. Should you need a more formal receipt at that point, please let us know by replying to this email.

Submitting prior to acceptance for a non-review workflow journal
Thanks for your interest in depositing your data in Dryad. Unfortunately, the way our system works right now, you must wait to submit to Dryad until your data are completely ready for archiving.

If you're planning to upload multiple files, you're welcome to get your submission started and save it as a draft in your personal Dryad workspace. This way you can continue to add to the submission by logging into Dryad and navigating to datadryad.org/submissions. But please make sure that your data are final and ready for archiving before clicking "submit."

We're working on a more flexible workflow for the future that will allow authors to upload data earlier in the publication process, but it is still in development.

Versioning questions
[data packages that must be versioned - simple cases] I can make the needed changes for you, but because your data is already part of the public archive, these changes will create a new *version* of your data package. Your doi will change slightly (an extension - .2 - will be added to the end of it, as doi:10.5061/dryad.t66ns.2), however, the original doi will still work. Any search for the original doi, or use of a link created with the original doi, will resolve to the data landing page for the newest version of your data package.

For an example of a versioned data package, see: http://dx.doi.org/10.5061/dryad.6169b.2. If you scroll to the bottom, you will see the version history. You can still access the original data package, but only by using the link at the bottom of the page.

Let me know if you would like to proceed with creating a new version of your data package.

___

[data packages that must be versioned - more complex cases] Thanks for contacting us. Ideally, we want authors to be able to revise and update their Dryad data packages. However, the versioning feature that will facilitate this capability is still in the development stage. So unfortunately, we have to wait to update your data package until the versioning feature is ready. This feature has taken much longer to develop, implement, and debug than we had expected, but we believe it will be ready soon. We'll add your data set to our list awaiting versioning. Thanks for supporting open data and Dryad. We regret the inconvenience this may cause you, and we hope that we'll be able to update your data set soon. ___

[very recently deposited data packages that only want to switch files] We're working on a versioning feature that will allow authors to update their data packages, but the feature isn't quite ready yet. We hope to roll out versioning sometime in 2014. Until the versioning feature is released, we generally don't like to change already-published data. However, because your data package was just published [VERY RECENTLY] and there are relatively few downloads on record, I think we can make an exception.

At this stage, a curator can only switch files (1-to-1). We can't add or delete files. Do you want to simply replace old files with new ones? If that's the case, please include the updated files as email attachments and clearly state which outdated files should be replaced by which updated files. I'll make the switch for you.

If you need to make more complex changes to your data package, I can add you to the list of data packages to be versioned. I must warn you though: these features often take much longer to develop, implement, and debug than expected.

Rejecting submission: Duplicate submission
The data associated with this submission has been archived at doi:XXXX.

Rejecting submission: No associated metadata email
Submission of data associated with [journal title] requires that the journal first send a description of your accepted manuscript to us. Either your manuscript is not at the correct stage for data archiving, or you need to contact your journal to opt in to using Dryad. Feel free to contact us at help@datadryad.org if you have any questions.

Rejecting submission: Submitter didn't use review workflow
Because your article is currently under review in [integrated journal], your data submission requires a different workflow. The easiest way to route your submission correctly is to resubmit using the Dryad link provided by your journal. You can also start a new submission, select article status "in review," and enter a valid manuscript ID. Submitting with the link or manuscript ID causes much of your information to be auto-filled, thus simplifying resubmission. Please contact us at help@datadryad.org if you have any questions.

Rejecting submission: Files are inappropriate for the repository
This submission is being sent back to you because [describe the problem and name the problem file if there is more than one file in the package]. We look forward seeing your submission again with an alternative data file. Please see the following page for information about what to deposit in Dryad: . Let us know if you have any questions.

Rejecting submission: Files have non-English content
We are ready to process your Dryad data submission; however, some of the content in your submission is not in English. [If you think it would be helpful, you may want to specify the problem and name the problem file if there is more than one file in the package]. At this time we are unable to accept datasets that are not in English. If you would please revise your file to translate the content into English and resubmit, we will be happy to continue processing your submission. Please contact help@datadryad.org with any questions.

Rejecting submission: Files have a non-CC0 license
Some of the content you uploaded is under a [specify license, usually GNU General Public License], which is incompatible with the Creative Commons Zero waiver required by Dryad and to which you agreed when initiating the submission. We welcome you to re-submit any content that you are able to release under CC0. [Additional explanation, if relevant.] Please contact help@datadryad.org with any questions.

Rejecting submission: Location information for endangered species
Some of the content you uploaded appears to contain information on rare and endangered species. It may be necessary to mask certain details (e.g., locations) to prevent any further threat to these natural resources. The following article may be helpful:

Lindenmayer D, Scheele B. Do not publish. Science 356(6340): 800-801 http://dx.doi.org/10.1126/science.aan1362

Please contact help@datadryad.org with any questions.

Rejecting submission: File is a manuscript
It appears you may have uploaded your manuscript. Dryad is a repository of data underlying publications and does not store the publications or manuscripts themselves. We welcome you to resubmit any underlying data. Please direct any questions to help@datadryad.org.

Rejecting submission: Human subject data not anonymized
It appears that the data files you submitted may contain personally identifiable human subject information. Data archived in Dryad is publicly available and any human subject data must be properly anonymized and prepared under applicable legal and ethical guidelines. We welcome you to resubmit any data that is appropriate for sharing.

For guidance, please read our FAQ on human subjects data at https://datadryad.org/pages/humanSubjectsData.

The following article may also be helpful:

Hrynaszkiewicz I ,Norton ML ,Vickers AJ ,Altman DG. Preparing raw clinical data for publication: guidance for journal editors, authors, and peer reviewers. BMJ 2010;340:c181 http://dx.doi.org/10.1136/bmj.c181

Declining to publish insufficiently anonymized data (Senior Curator only)
''After sending the above rejection notice once or twice without satisfactory results, Dryad reserves the right to decline to publish the data. Please reject the submission using the following template:''

Dryad declines to publish this data, due to concerns about personally identifiable information. For more details, please see the email sent on x/xx/xxxx, from curator@datadryad.org, titled "Your Dryad submission: Decline to publish."

Then send a separate email to the author and the publisher from curator@datadryad.org, using the following template:

Subject: Your Dryad submission: Decline to publish

Dear [author]

We appreciate your taking the time to revise your data submission. However, we still have concerns that your data may not meet anonymization standards. [Explain specifics, e.g. In your case, the number of indirect identifiers and the small sample population make anonymization difficult.] We therefore decline to publish your data set, and we are returning the submission to your Dryad workspace.

Dryad is under no obligation to assure that the data published in the repository are free of personally identifiable information (please see Terms of Service, Sections 6.2 and 3.3), but we reserve the right to decline to publish data that appears non-compliant with published standards for anonymizing data, such as:

'''Hrynaszkiewicz I ,Norton ML ,Vickers AJ ,Altman DG. Preparing raw clinical data for publication: guidance for journal editors, authors, and peer reviewers. BMJ 2010;340:c181 http://dx.doi.org/10.1136/bmj.c181'''

If, in consultation with your editor, you decide that proper anonymization of your data is possible, please feel free to revise your data and resubmit. Thank you for your interest in Dryad, and we hope you will think of us when archiving data in the future. If you have any questions, please contact us at help@datadryad.org.

Best wishes, [Senior Curator]

Rejecting submission: Incomplete GIS data
This submission is being sent back to you because I was unable to open the following files included in this package:

[file_name.shp] [file_name.mxd]

Since these files are incomplete portions of ArcGIS documents, please include all associated files along with the .shp or .mxd files for this item when re-submitting this data package. We look forward seeing your submission again, and let us know if you have any questions.

Rejecting submission: Duplicate submission
It appears that you submitted multiple data packages for the same set of data. Dryad only allows for one data package per published article so that all data related to that article will be archived together in one place. All duplicate submissions have been consolidated and archived in data package [doi:XXX]. Let us know if you have any questions.

Rejecting submission: Associated article has been published in another journal
It appears that the article associated with your data package has been published in a journal different from the one you originally submitted under. You submitted your data as being published in [journal name], but we found the article published in [journal name]. We are sending your submission back to you so that you may edit your publication metadata, and we welcome you to resubmit if your new journal also wishes you to archive your data. If you have any questions, please direct them to help@datadryad.org.

Potentially inappropriate files: Content from the article
I'm ready to approve your Dryad submission and assign a DOI, but wanted to ask about the following file that you uploaded: [file name]

It appears that this file may contain content from the manuscript itself [or more specific phrasing], which would be inappropriate to release under Creative Commons Zero.

Please see the following page for information about what to deposit in Dryad: http://www.datadryad.org/pages/faq#depositing-acceptable-data

and the following page for information about the Creative Commons Zero terms: http://creativecommons.org/about/cc0

Please let me know if you would like to provide alternative data files, or if you have any questions about the type of files to submit, why Dryad asks you to release your files from copyright restrictions, and any other concerns you may have.

Potentially inappropriate files: Data not ready for analysis
I'm ready to approve your Dryad submission and assign a DOI, but wanted to ask if you would be able to provide your data files in an alternate format, such as [give appropriate examples based on their file, like CSV, tab delimited, plain text]. Data in Dryad should be submitted in a state that is ready for analysis and optimal for reuse, so [the file format they submitted] is not ideal. Thanks for considering this request.

Potentially inappropriate files: Human subject data
Dear [ ],

We are ready to approve and archive your Dryad submission, but first need you to confirm that the files you submitted do not contain any personally identifiable human subject information. Data archived in Dryad is publicly available and any human subject data must be properly anonymized and prepared under applicable legal and ethical guidelines. Please let us know if you need to revise your submission. The following article may be helpful: http://dx.doi.org/10.1136/bmj.c181

Best wishes, [ ]

Potentially inappropriate files: Rare proprietary formats
We have received your data package submission, but we are unable to review it because of the proprietary [.XYZ] file type. Although Dryad will accept proprietary file formats, our mission of open access and preservation leads us to prefer files in more common or open source formats, such as .txt, .csv, or .xls. If it is possible to submit your data in an alternative format, it would be greatly appreciated. If not, we can archive it in its current format, but we cannot guarantee its stability or interpretability over time. If you can provide alternative files, please email them to help@datadryad.org and we will replace the files in your current submission. If you have any questions, please contact us at help@datadryad.org<[mailto:help@datadryad.org mailto:help@datadryad.org]

Unspecified custom embargo
Dear [AUTHOR], I am writing in regard to data from “ARTICLE TITLE HERE” (doi:ADD DRYAD DOI HERE)

You have selected a custom embargo for your data files. Our standard embargo lengths are “until article appears” and “one year”. Embargoes longer than one year generally require permission of the journal’s editorial office. We have set your embargo to lift one year from the date your article is first published online. If you would like a longer embargo, please let us know what you had in mind.

Thank you for choosing to archive and share your data!

Email for submissions approved into publication blackout
Subject: Dryad submission approved pending publication doi:10.5061/dryad.NNNN

Dear [Depositor name],

Your submission to the Dryad repository has been approved, and will be available in the repository once the associated article has been published. Your data package has been approved and assigned a unique identifier, called a DOI.

Title: Data from: [Title] Data identifier: [DOI] Journal manuscript number: [MS#]

You will receive another email when your data is made available. If you did not request a data embargo, your data will be publicly available after the article is published.

Ensure that your readers can find your data!

We recommend that the article include a link to the Dryad data as follows: Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.NNNNN

Check out the information for depositors at http://datadryad.org/pages/faq - How do I refer to my Dryad data in my article? - How can I see how often my data package is viewed and downloaded? - How can I add my data package to a Data section on my CV? - If my data files are embargoed, when will they be released? - and more!

Thanks again for taking this important step to preserve and share your research data. We welcome your feedback! Contact us at help@datadryad.org.

The Dryad Team datadryad.org

Email for integrated submissions (no publication blackout)
Subject: Dryad submission approved [DOI]

Dear [Depositor name],

Thank you for your submission to the Dryad Digital Repository. Your data package has been approved and assigned a unique identifier, called a DOI.

Title: Data from: [Title] Data identifier: [DOI] Journal manuscript number: [MS#]

Ensure that your readers can find your data!

We recommend that the article include a link to the Dryad data as follows: Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.NNNNN

Your journal may follow the CrossRef recommendation that the data package be cited in the article reference list. If so, the citation should include the Dryad package DOI, e.g.:

Author(s), Year, Data from [title]. Dryad Digital Repository [DOI]

To view your Dryad entry, you may visit the repository at http://datadryad.org

Check out the information for depositors at http://datadryad.org/pages/faq - How do I refer to my Dryad data in my article? - How can I see how often my data package is viewed and downloaded? - How can I add my data package to a Data section on my CV? - If my data files are embargoed, when will they be released? - and more!

Thanks again for taking this important step to preserve and share your research data. We welcome your feedback! Contact us at help@datadryad.org.

The Dryad Team datadryad.org

Weekly integration report
In the week since the last report (YYYY-MM-DD), Dryad has received the following.

New notifications of accepted publications in this journal: #

New deposits associated with publications in this journal: #

Please find the data DOIs for new deposits below, for inclusion in the published articles.

Author manuscript# DOI

Author manuscript# DOI

We recommend that journals include a link in the article to the Dryad data as follows:

Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.NNNNN

Dryad links the data files to the published articles; it is up to journals to link published articles to their supporting data. Journal staff and authors collaborate to ensure that data DOIs are included in the appropriate locations for the print and online versions of published articles.

Thank you!

FTP transfer for large files (over 1.5 GB)
Create a separate directory via the command line for each user that asks for FTP instructions.


 * 1) SSH to either ehull@ftp.datadryad.org or eclary@ftp.datadryad.org
 * 2) Once there, `cd /dryad-data/transfer`
 * 3) Use the submitter's last name for the directory name, all lowercase, and create the directory inside the transfer directory: `sudo mkdir FOLDERNAME`
 * 4) Change the permissions on the new directory: `sudo chmod 777 FOLDERNAME`
 * 5) Be sure to replace the 2 instances of "FOLDERNAME" below with the actual folder name. Send the following instructions to the submitter:

Thank you for contacting us. Dryad is currently unable to accept files >1.5GB through the main web interface. Please submit your large files via Secure File Transfer Protocol (SFTP) using the instructions below.

First, please make note of the following as you prepare your files:
 * File sizes (or directory of files) should be no larger than ~10GB to ensure accessibility. Organize and split directories of files as needed.
 * Create a compressed file archive of your files. Large ZIP files (>4GB) can be problematic to extract, so we recommend using an alternate format (e.g., .tar.gz, .gz, .7z).
 * Please include the name and version of the software used to create the file archive in your README.
 * Verify your file archive extracts correctly and without error before uploading. You can also run integrity checks with many compression applications.
 * Dryad charges excess storage fees for data packages totaling over 20GB. The fee is $50 for each additional 10GB, or part thereof. Overage fees are payable by the submitter, even if the base publishing charge is covered by the journal or another sponsor 

Second, complete your current Dryad submission by uploading dummy placeholder plain-text files in place of any file you're submitting via SFTP.
 * Name the dummy files so that they match the real filenames, with "REPLACE" added to the filename (e.g., “Dataset-REPLACE.txt”). These files can contain a simple sentence like "This file should be replaced."
 * Complete the description fields associated with the dummy files to reflect the content of your actual data files.
 * Once the submission is completed and we have received the larger files via SFTP, Dryad staff will overwrite the dummy files.

Last, upload your large files to the Dryad FTP server. We have created a directory for your files using your last name (e.g., “/dryad-data/transfer/Appleseed”). To access it, you will need the following information:

Hostname: sftp://ftp.datadryad.org Username: transfer Password: XXXXXXXX

Connect using an FTP client (e.g., FileZilla (https://filezilla-project.org/). Local site : {directory/where/files/are/located} Remote site: /dryad-data/transfer/{submitters_last_name} Click and drag files you want to transfer

Or, connect using the command line. Open a Terminal window and type the following: > cd {directory/where/files/are/located} > sftp transfer@ftp.datadryad.org > XXXXXXXX > cd /dryad-data/transfer/{submitters_last_name} > put {files_to_transfer} > exit

NOTE: When the transfer process has completed, your file(s) will be moved to another secure server, and will no longer be visible in your directory.

Please let us know if you need any help.

General intro to Dryad integration and membership
We'd be delighted to pursue integration with Dryad for JOURNAL. Authors are welcome to deposit data in Dryad associated with any published (or soon to be published article), but the greatest efficiencies come from connections we can build together, between the journal and the Dryad repository. Our process involves implementing coordinated data submission along with manuscript review; this shortcuts the process for authors to submit their data, and ensures that there are permanent links between articles and their data. It's also possible to make data available during the peer review process, if a journal wishes to do so. The Dryad team would be pleased to see how we can be of service to JOURNAL.

Below is some background and links regarding the implementation of integration between your journal and the Dryad repository, and membership in the Dryad organization.

INTEGRATION WITH DRYAD

Integration with Dryad allows journals to facilitate data archiving by setting up automatic notifications to Dryad from the journals' manuscript submission system. Advantages of integration include:


 * streamlining the authors’ data deposit process
 * permanently linking the published article with its securely archived data
 * allowing authors to deposit complex and varied data types in robust re-usable formats
 * ensuring that data files are discoverable, indexed, and exposed to both web and bibliographic search engines
 * enhancing visibility of the article via linking from the data files
 * permitting embargoes to delay release of data, in accordance with journal policy

There is no charge for implementing this integration process, and membership in Dryad is not required for integration of manuscript and data submission. The journal's editorial system sends automated notices to Dryad, providing the details of manuscripts under review or accepted, so Dryad can create a provisional record for the data, and the journal invites the authors to upload their data to Dryad. There are several optional customizations available, such allowing reviewers and editors access to the data during the review process, and enabling or prohibiting embargoes

I have attached a few slides that illustrate the primary workflows. We invite you to review our complete documentation at http://wiki.datadryad.org/Submission_Integration. The steps to implementation of integration with Dryad are:


 * Initial planning discussions
 * Journal completes the Pre-Integration Questionnaire (relaying journal parameters and options)
 * Testing of journal notices to Dryad, reiterate until problems are resolved
 * Rollout to authors & ongoing integration

The usual time to implement this process can be as little as a few weeks; it's really just a matter of making sure that the notices we exchange are error-free.

Please feel free to browse and search the repository to see how it looks: http://datadryad.org/ [As of DATE Dryad contains XXXX data packages and XXX data files, associated with articles in XXX journals.] There's already XXX article from/s JOURNAL with associated data in Dryad: http://dx.doi.org/10.5061/dryad.XXXX This data was voluntarily submitted by the authors last year.

MEMBERSHIP IN THE DRYAD ORGANIZATION

Dryad is both a repository and an organization. The organization consists of an international consortium of stakeholders, including journals, publishers and scientific societies, and provides a forum for all stakeholders to share knowledge and coordinate action around data policies. Dryad endeavors to ensure that all stakeholders are both contributing to and receiving the benefits of data archiving. It makes data archiving low-burden and high reward for researchers in a number of ways - for example, through a strong data citation policy, tracking of downloads, and enabling data authors to receive first authorship.

Partnership with Dryad is of value to journals and publishers because it provides a level of service well beyond that of Supplementary Materials - data can be independently discovered but have prominent links back to the original article, DataCite DOIs are assigned and included within the articles, metadata is curated, data files may be versioned, files are migrated to avoid format obsolescence, data can be made available for peer review, data embargoes can be honored, and so on. Dryad empowers its stakeholders in governance, so it is responsive to their needs, and it takes seriously the need for sustainability and long-term preservation.

Publishers, societies and journals can become Dryad partners through membership in Dryad; Dryad has incorporated as a not-for-profit organization in the US. Dryad members receive a discounted rate for data deposits, select the Board Of Directors and receive the benefits of participation in membership forums. Membership information and pricing details are available on our website.

I will be glad to answer questions about membership and integration, and would be happy to set up a phone or Skype call with you if that would be helpful. Please let us know what questions you have and how you would like to proceed. Thanks again for your interest in Dryad and your support for data archiving. We look forward to hearing from you.

Welcome to the Dryad Partners list
I've added you to the Dryad Partners email list. This is a list for use by Dryad partner journals and publishers, who occasionally ask questions or share practices about issues relating to Dryad. Subscribers to the list are editors, managing editors and others involved in the editorial and production processes in journals that are sending metadata to Dryad, or planning to do so soon. There's not much traffic on the list-- it has been a good sounding board so far, for questions about revising journal instructions to authors to include reference to Dryad, etc. Dryad staff are also subscribed to the list and sometimes we use the list to get partner feedback or announce developments. The list address is partners@datadryad.org if you'd like to send a message or a question any time. Please let me know if you'd like to suggest anyone else that we should add.

As background about Dryad I'd like to be sure you are aware of the resources we have available. Here's a short overview:


 * on the repository website at http://www.datadryad.org/ in the left sidebar there's an About page as well as pages with info for depositors & users of data
 * the Dryad wiki at https://wiki.datadryad.org contains documentation about the project, almost all of it open
 * the Dryad blog at http://blog.datadryad.org/ carries news and updates about the repository and data archiving in general
 * the Dryad team members are all happy to hear from you too, and the best way to reach someone is the general email address: help@datadryad.org

Thanks again and we look forward to working with you.

Responding to journals about using the two-step process
Regarding your suggestion that authors should agree to data archiving before an email is sent: You are welcome to do this, as it creates no technical problems. We have a few other journals using this process. However, in our experience, it creates a significant amount of confusion for the authors. Many authors will neglect to select the data archiving option in your system, but later decide to archive their data. These authors then come directly to Dryad and find that their manuscript number is rejected as "invalid", since we have not received any information about the submission. We are happy to inform these authors that they must return to you and request the metadata be sent, but some authors will give up at this point, resulting in a lower rate of data archiving.

Longer version:

Integration with Dryad begins with notices from the journal's manuscript processing system to Dryad relaying manuscript bibliographic details, allowing Dryad to create provisional records in anticipation of authors depositing the data. At the same time, the journal invites authors to deposit data in Dryad, and provides a link to the Dryad provisional record.

Most journals send notices to Dryad for all the manuscripts they consider, as this allows them to automate this step as a part of their routine manuscript review process. Notifying Dryad of all manuscripts under consideration has the benefit that the authors may chose later to deposit data in Dryad, perhaps in response to reviewer request, and their provisional record will be ready for them.

Some journals have preferred to ask prior author permission to share manuscript details with Dryad, and only sending us the initial notice of manuscript details when authors agree. (We do support this workflow and offer templates for modifying Manuscript Central accordingly.) However, in our experience this two-step process can lead to several problems: first, a low participation rate, as many authors don't know what Dryad is at the time they are submitting a manuscript, and tend to opt out. Additionally, it causes delays and frustration for all concerned when authors who opted out initially later decide to deposit in Dryad, go to our submission system, but find that Dryad doesn't have any record of their manuscript. The author complains to Dryad, we go back to the journal and ask them to send us a notice for the manuscript, and then we ask the author to try again. Only the most determined authors will actual deposit data in this scenario. All this back & forth is tedious, and can delay the availability of the data and the inclusion of the Dryad DOI in the published article.

For all these reasons we prefer to receive notices from journals for all manuscripts under consideration. Dryad keeps all these records hidden from public view until the data has been submitted, approved by our curators, and the associated article has been published.

A sample message to authors from a journal that uses the two-step process emphasizes the benefits to authors:

"JOURNAL supports open access to raw data. Publishing your full dataset can boost citations, improve transparency and further scientific progress. The Dryad data repository will securely preserve and publish your dataset as a citable entry in the scientific record. With your consent we will pass your manuscript’s details to Dryad. You will then receive a link to access Dryad and upload your dataset. After successful deposition a unique DOI for the data will be assigned for inclusion in the data sharing section of your article. All data should be suitably anonymised. Find out more here."

Information about other repositories
Other repositories might be worth your consideration, for example Zenodo https://zenodo.org/. Also Figshare http://figshare.com/ allows anyone to share any research content.

There are at least 2 big indices of research repositories which you can browse and search: Re3data http://www.re3data.org/ and also Databib http://databib.org/.

Information about data journals
Each submission to Dryad must be associated with a publication. We are glad to offer some suggestions for publication, in particular, data journals that might publish your findings and enable you to deposit the associated data in Dryad.

There is an emerging practice of journals publishing data papers, or descriptions of datasets, while the data files themselves are held in a repository like Dryad.

''A data paper is a journal publication whose primary purpose is to describe data, rather than to report a research investigation. As such, it contains facts about data, not hypotheses and arguments in support of those hypotheses based on data, as found in a conventional research article. Its purposes are threefold: to provide a citable journal publication that brings scholarly credit to data publishers; to describe the data in a structured human-readable form; and to bring the existence of the data to the attention of the scholarly community.''

From: Vishwas Chavan and Lyubomir Penev, The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics 2011, 12(Suppl 15):S2. http://dx.doi.org/10.1186/1471-2105-12-S15-S2

''A data paper is a publication that is designed to make other researchers aware of data that is of potential use to them. As such it describes the methods used to create the dataset, its structure, its reuse potential, and a link to its location in a repository. It is important to note that a data paper does not replace a research article, but rather complements it. When mentioning the data behind a study, a research paper should reference the data paper for further details. The data paper similarly should contain references to any research papers associated with the dataset.''

From: Open Health Data

Summarizing your data in a data paper and publishing that description in one of these journals would meet Dryad’s requirement that the data be associated with a publication.

Data journals, and journals that publish data papers, in the biological sciences include:

Biodiversity Data Journal http://www.pensoft.net/journals/bdj/ and other journals from Pensoft Publishers http://www.pensoft.net/


 * Zookeys
 * PhytoKeys
 * MycoKeys
 * BioRisk
 * NeoBiota
 * Nature Conservation
 * See also the Pensoft statement on Data publishing, at http://www.pensoft.net/page.php?P=23

BioInvasions Records http://www.reabic.net/journals/bir/

BMC Research Notes http://www.biomedcentral.com/bmcresnotes/about

CODATA's Data Science Journal http://www.codata.org/dsj/index.html

Dataset Papers in Biology http://www.hindawi.com/dpis/biology/

Datasets Papers in Ecology http://www.datasets.com/journals/ecology/

Earth System Science Data http://www.earth-system-science-data.net/

Ecological Archives http://esapubs.org/archive/

eLife http://www.elifesciences.org/

F1000 Research http://f1000research.com

GigaScience http://www.gigasciencejournal.com/

Marine Biodiversity Records http://journals.cambridge.org/action/displayJournal?jid=MBD

Open Health Data http://openhealthdata.metajnl.com/

PLOS Data Pages (forthcoming) http://www.plos.org/

Thanks again for your inquiry and for your interest in depositing your data in Dryad.

Dryad and Data Management Plans
We encourage you to make Dryad part of your Data Management Plan (DMP) when applying for your next grant. We also encourage you to take advantage of datatype-specific community standards and repositories when they exist. Biosharing (http://www.biosharing.org/) provides a searchable registry of data standards and repositories in life sciences and biomedicine. Re3Data (http://www.re3data.org/) provides a list of research data repositories across all disciplines. Free, online tools such as DMPTool (https://dmp.cdlib.org/) and DMPOnline (https://dmponline.dcc.ac.uk/) can help you prepare a quality data management plan that is customized to your specific funder guidelines.

You may use the following text verbatim or customize it for your DMP: EDIT THIS TO BE BOILERPLATE: Data underlying publications that is not submitted to a specialized repository will be deposited in Dryad. Dryad provides the following features... Data are released upon publication and made freely available under a Creative Commons Zero waiver without restrictions on access or reuse. Data is discoverable, and assured of availability long-term. ...

Budget for Data Publication charges (DPC). The base DPC is $80 per data package, although in many cases the base DPC will be paid by a sponsoring organization (http://datadryad.org/pages/integratedJournals). If the files in the data package are collectively over 10GB, then an excess storage charge will apply ($15 for the first and $10 for every GB thereafter). If you submit to a journal that lacks submission integration, an additional $10 fee will apply (http://datadryad.org/pages/pricing). &lt;/pre&gt;

Takedown requests
Thank you for bringing the issue with this data package to our attention. The retraction of publicly-available data that has been part of the scholarly record is not something we take lightly, or that happens very often (in our experience), so we want to be sure it is handled carefully.

Please see our Terms of Service for a list of requirements in order to take down content: https://datadryad.org/pages/policies#retraction I must ask you to follow as precisely as possible the procedures laid out at the link above. Once we receive those materials, we will consult internally and determine the proper course of action.