Difference between revisions of "Templates for Correspondence"

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Data deposited in the Dryad Repository: http://dx.doi.org/{####}
 
Data deposited in the Dryad Repository: http://dx.doi.org/{####}
  
I invite you to contact me as soon as possible when your article is published, as your Dryad data package will not become public until we finalize the record with article citation information. We are working to streamline this process for journals that aren't sending information about their articles to Dryad, such as {Journal title}. You may receive a redundant, automatically generated notification when your data package enters the public archive.
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I invite you to contact us as soon as possible when your article is published, as your Dryad data package will not become public until we finalize the record with article citation information. We are working to streamline this process for journals that aren't sending information about their articles to Dryad, such as {Journal title}. You may receive a redundant, automatically generated notification when your data package enters the public archive.
  
 
Thanks for choosing to archive and share your data!
 
Thanks for choosing to archive and share your data!

Revision as of 07:17, 16 April 2013

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


Contents

Responding about receiving the verification email 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. 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: <http://datadryad.org/forgot>.

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.

Responding to questions about author fees

June 2012

Thank you for your inquiry about the costs of data deposition to Dryad, and for planning to deposit your data in Dryad. We're not able to give you a totally firm answer because the Dryad Board of Directors has not yet approved the proposed fee schedule, however the anticipated author deposit fee is $50- $100 per data package. (A data package = all the data associated with an article.) Additional charges may apply if the data package exceeds 10 GB. The draft fee structure is summarized here.

Please note that author fees would only apply when the associated article/s are not published in a Dryad member journal that has a contract with Dryad to cover data archiving costs. We understand the unpredictability involved in this, and your need to plan for this eventuality. Our fee structure is based on Dryad members supporting the costs of the repository, and reducing the barriers to authors' data archiving. Dryad members will also include research institutions and funding organizations, which will be able to purchase vouchers to cover the costs of author fees when the journal is not a Dryad member.

Thanks again for planning on depositing in Dryad, and please let me know if you have further questions. Good luck with your proposal!

Responding to questions about 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.



Responding to depositors who haven't opted in to having their article metadata sent to Dryad

Some journals, and [journal title] is one of these, require authors to accept their invitation to use Dryad before they send us the description of your manuscript. There should have been something in your manuscript acceptance message asking if you'd like to deposit data in Dryad. You can email the journal editors and they will send you a link to your pre-populated Dryad submission. Please note that you'll have to log in before proceeding with the submission.

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

Responding to depositors who are using the "short" manuscript number for a journal that requires "extended" manuscript numbers

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.

Responding to depositors who need to create an account and 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.


Responding to depositor who needs to submit new files to an item in "Journal Review" status

You can add the corrected files to your data package, and we will remove the outdated files during the curation 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 may see the files that were originally submitted.

To add the corrected files, login to 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 reply to this message 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 outdated files.

Rejecting submission because there is no associated metadata email

Submission of data to Dryad associated with [journal title] requires that the journal first send a description of your manuscript to us. Either you have not opted in to using Dryad with the journal, or your manuscript is not yet at the appropriate stage for data archiving. Please use the submission link provided by the journal or enter a valid manuscript ID. Feel free to contact us at help@datadryad.org if you have any questions.

Rejecting submission because 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: <http://www.datadryad.org/depositing>. Let us know if you have any questions.

Rejecting submission because files are inappropriate for the repository (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 because files are inappropriate for the repository (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 because files are inappropriate for the repository (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. The following article may be helpful: http://dx.doi.org/10.1136/bmj.c181

Rejecting submission because files include 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.

Asking depositor about 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/depositing

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.

Asking depositor about 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.

Asking depositor about 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, [ ]

Author email for queued (publication blackout) non-integrated submissions

Subject: Dryad submission accepted {doi:10.5061/dryad.####}

Dear {Depositor Name},

We are pleased to archive your data associated with "{Article title}" in Dryad. Once your article is published, your Dryad data package will be made public {note here if they selected one year embargo} and your data DOI will be registered. We encourage you to add this DOI to the final version of your article, as shown below.

Data deposited in the Dryad Repository: http://dx.doi.org/{####}

I invite you to contact us as soon as possible when your article is published, as your Dryad data package will not become public until we finalize the record with article citation information. We are working to streamline this process for journals that aren't sending information about their articles to Dryad, such as {Journal title}. You may receive a redundant, automatically generated notification when your data package enters the public archive.

Thanks for choosing to archive and share your data!

Author and journal rep email for queued (publication blackout) integrated submissions

Subject: Dryad submission accepted {doi:10.5061/dryad.####}

Dear {Depositor Name},

Thank you for your recent submission to the Dryad repository. Your data package has been approved and assigned a unique identifier, called a DOI, though it will be hidden from public view until the associated article is published. You may receive a redundant approval message when your data enters the public repository.

Title: {Article title}

Data identifier: {doi:10.5061/dryad.####}

Journal manuscript number: {manuscript number}

We recommend you add text to your article specifying the location of the data, for example:

Data deposited in the Dryad repository: http://dx.doi.org/{####}

Check out the information for depositors at http://www.datadryad.org/depositing

  • 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.

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


The DOI may be presented as below:

Data deposited in the Dryad repository: http://dx.doi.org/10.5061/dryad.####


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!

Alternate upload through FTP

Dryad is currently unable to accept files over 2GB through the main web interface. Instead, please
submit your files via FTP, using the instructions below.

Please complete your current Dryad submission using dummy plain text files. These files can
contain a simple sentence like "This file should be replaced." You can name the dummy files so
that they match the real files, with "replace" added to the file name or a similar scheme. Please
complete the other description associated with the dummy files to reflect the content of the actual
files.

Once the submission is completed and we have received the larger files via FTP, Dryad staff will
replace the dummy files. Let me know if you need further clarification or if you encounter any trouble.

FTP Instructions:

We have set up an FTP service that will enable you to transfer large files to Dryad. You can use any
standard FTP software, including software that typically comes pre-installed on most personal
computers.

Hostname: datadryad.org
Username: XXXXXXXX
Password: XXXXXXXX

Instructions for Macintosh OS X:
Launch the Terminal program, which appears in the Applications folder under the Utilities folder.
At the Terminal prompt, change the current directory so that you are same directory as the file you
want to send.
Enter "ftp datadryad.org" (without the quotes).
Enter the username and password listed above.
Type "bin" to enable binary transfer mode.
Type "put myfile.txt", replacing myfile.txt with the name of your actual file.
After the transfer is complete, type "quit" to exit the FTP program and close the Terminal application.

Instructions for Windows:
http://windows.microsoft.com/en-US/Windows7/Work-with-files-on-an-FTP-site
(for the site name, use FTP://datadryad.org)
Once you have connected to the FTP site, you can drag your data files into the connected folder.

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; we are in the process of incorporating as a not-for-profit organization in the US and details will be finalized and publicized next month, so we expect to be able to welcome new members later in the year. Dryad members will receive a discounted rate for data deposits, select the Board Of Directors and receive the benefits of participation in membership forums. Annual membership dues of $1000 USD will help defray the communication and meeting costs associated with a large membership-based organization. The charges for data deposits are not yet set, but we expect they will be approximately $50 USD per data package (all the data associated with a given article.) I will ensure that you receive more information about Dryad's membership and payment plans as soon as it is available. Currently no fees are being charged for any Dryad services.

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 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: The Journal of Open Public 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/

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

Datasets International http://www.datasets.com/journals

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/

Journal of Open Public Health Data http://openpublichealthdata.metajnl.com/about/

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

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

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