Submission Integration: Implementation

The steps required to set up, test, roll out, and manage submission integration are described on this page.

Initial planning
Journals initiating submission integration should [mailto:director@datadryad.org contact Dryad staff] to discuss the details of the process, and to fill out the Pre-Integration Questionnaire. Some of the issues to discuss include:


 * Summarize workflow options, confirm journal preferences (embargoes, data available during the review process, etc.)
 * How and when the journal will provide automated email notifications to Dryad of new manuscripts. Most journals opt to do this at the time of acceptance.
 * How the journal will invite authors to deposit data, and provide the Dryad submission system URL.
 * Where the journal will include the Dryad DOI in the published articles.
 * Whether/how the journal will monitor or enforce timeliness of deposition.
 * List of journal representatives that will receive reports from Dryad, including immediate notifications of Dryad submissions and weekly summary reports.
 * How Dryad will monitor the final publication of articles (so Dryad curators can complete the bibliographic details in the Dryad record).
 * The timeline for testing the process and for implementation with authors.

Overview of the basic workflow: data submission after article acceptance

 * 1) Author submits manuscript to journal.
 * 2) Journal sends notice to the Dryad system for each accepted manuscript (see details); Dryad uses it to create a provisional record for the anticipated data.
 * 3) Journal provides the author with a Dryad submission system link, and invites them to submit data. This custom link takes the author to their provisional entry in Dryad, incorporating the information supplied by the journal notice.
 * 4) *format for the submission link to Dryad: http://datadryad.org/submit?journalID=ABCD&amp;manu=NNNN (where ABCD is replaced by the journal code and NNNN is replaced with a real manuscript number that exactly matches the "MS Reference Number" field sent to Dryad)
 * 5) *sample text for use with authors is available, describing the benefits of data deposit in Dryad
 * 6) *note that the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
 * 7) Author uses the custom link to access the provisional Dryad record (with manuscript info pre-filled), uploads data files, and submits data package to Dryad.
 * 8) Dryad assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal immediately upon submission (see email template).
 * 9) Dryad curators review the data, performing basic checks on each file, and approve the release of the data package.
 * 10) Journal includes the Dryad data reference with DOI in all print and online versions of published articles.
 * 11) *Dryad suggests, following CrossRef and BioMed Central recommendations, that the DOI be included as an in-text citation, and additionally that the full data citation be listed in the references section of the article. This will ensure that the data is permanently accessible, and will make it easier to find data references within the journal and other scholarly literature.
 * 12) **suggested format for citation in article text:
 * 13) ***Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.j512f21p
 * 14) **suggested format for citation in Reference list:
 * 15) ***Sadd BM (2011) Data from: Food-environment mediates the outcome of specific interactions between a bumblebee and its trypanosome parasite. Dryad Digital Repository. http://doi.org/10.5061/dryad.t903h
 * 16) Dryad makes the data public in accordance with journal preferences. Dryad will provide any information the journal may need to verify deposits, but enforcement of deposition policy is up to the journal.
 * 17) Dryad sends the journal weekly reports with DOIs for any new data submissions associated with its articles.

Overview of the review workflow
The review workflow allows a journal to have editorial oversight of data in Dryad associated with its articles while the manuscript is in review, and also enables peer reviewers access to the data. Data files are submitted to Dryad while the manuscript is in review, and authors can add new versions of files to respond to editorial or reviewers' concerns.

Journals using the review workflow typically send two notices to Dryad for each manuscript: the first at manuscript submission, and a second at manuscript acceptance or rejection. Dryad curators do not review the data until the journal sends the second notice relaying the acceptance of the manuscript. If the manuscript is rejected, Dryad returns the data to the authors' workspace, where it can be later associated with another journal.


 * 1) Author submits manuscript to journal.
 * 2) Journal sends notice to the Dryad system for all submitted manuscripts (see details); Dryad creates a provisional record for the anticipated data.
 * 3) Journal provides the author with a Dryad submission system link, and invites them to submit data. This custom link takes the author to their provisional entry in Dryad, incorporating the information supplied by the journal notice.
 * 4) *format for the submission link to Dryad: http://datadryad.org/submit?journalID=ABCD&amp;manu=NNNN (where ABCD is replaced by the journal code and NNNN is replaced with a real manuscript number that exactly matches the "MS Reference Number" field sent to Dryad)
 * 5) *sample text for use with authors is available, describing the benefits of data deposit in Dryad
 * 6) *note that the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
 * 7) Author uses the custom link to access the provisional Dryad record (with manuscript info pre-filled), uploads data files, and submits data package to Dryad.
 * 8) Dryad assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal immediately upon submission, along with a temporary, secure review URL where journal reviewers and editors may access the data (see email template).
 * 9) Journal either accepts or rejects the manuscript, and notifies both the author and Dryad of the decision.
 * 10) *the second notice includes the same fields as the first one (see details ), but with Article Status: either "accepted" or "rejected"
 * 11) *the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
 * 12) Dryad curators process and approve the data files and register the DOI if the MS is accepted (see notification email template).
 * 13) *If the MS or data package is rejected, the submission is returned to the submitter's personal workspace (see notification email template).
 * 14) Journal includes the Dryad data reference with DOI in all print and online versions of published articles.
 * 15) *Dryad suggests, following CrossRef and BioMed Central recommendations, that the DOI be included as an in-text citation, and additionally that the full data citation be listed in the reference section of the article. This will ensure that the data is permanently accessible, and will make it easier to find data references within the journal and other scholarly literature.
 * 16) **suggested format for citation in article text:
 * 17) ***Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.j512f21p
 * 18) **suggested format for citation in Reference list:
 * 19) ***Sadd BM (2011) Data from: Food-environment mediates the outcome of specific interactions between a bumblebee and its trypanosome parasite. Dryad Digital Repository. http://doi.org/10.5061/dryad.t903h
 * 20) Dryad makes the data public in accordance with journal preferences. Dryad will provide any information the journal may need to verify deposits, but enforcement of deposition policy is up to the journal.
 * 21) Dryad sends the journal weekly reports with DOIs for any new data submissions associated with its articles.

Dryad-first option
Some journals require authors to deposit and/or publish data before manuscripts are considered for publication. For these journals, we offer a "Dryad-first" option wherein authors can submit data to Dryad without a manuscript number and receive a Dryad DOI to include with their MS submission, along with a temporary data review link.

This option allows for data review but does not the include first notice from the journal to Dryad (as described above), the creation of the provisional Dryad record or the custom journal invitation/submission link, meaning that authors must provide information about their MS to Dryad manually. Please [mailto:journalsetup@datadryad.org contact us] to discuss the details.


 * See details of the review workflow using the Dryad-first and REST API options

Testing the format of journal notices
The journal sends one or more test notices to Dryad, to ensure that both systems are communicating without problems. These messages will handled automatically by the Dryad submission system, not read by a human, so they must conform to the format requirements or they will not be processed correctly.

For the format requirements for all notices to Dryad, see the Journal Metadata page.

This is the testing process:


 * 1) The journal sends several test article notifications, and Dryad creates new records in a testing environment.
 * 2) *Ideally, testing should include several test messages, at least with one multiple authors, and using different settings for Article Status, to ensure that these cases are processed correctly.
 * 3) Dryad staff and journal representatives test the notifications, specifically the integrity of the information transfer to Dryad.
 * 4) Any problems that are discovered are resolved, and testing is repeated until no more issues are found.

Timing of data release
When the journal notifies Dryad that an article has been accepted, our curators then process and approve the associated data submission into the Dryad archive, at which point the Dryad DOI is registered. Prior to article publication, there are 2 options for data package display on the Dryad website:


 * 1) Option 1: Dryad publishes the data package -- including provisional information about the article -- immediately upon article acceptance. If the journal has opted to allow data embargoes, authors may choose to disallow download of the data files until article publication.
 * 2) Option 2: Dryad withholds public release of the data package until the associated article is published. We call this option “publication blackout.” The Dryad DOI is functional during this stage, but redirects to this page: http://datadryad.org/pages/publicationBlackout

We define “article publication” as the point at which it first becomes available online. As soon as we become aware that the article is online, we will release all metadata and data files (assuming no longer-term data embargoes are in place).

To see how other integrated journals handle this, see http://datadryad.org/pages/journalLookup (the “Metadata hidden until publication” policy).

Implementation of integration and rollout to authors
When the testing phase is complete and all the desired customizations have been implemented, Dryad will inform the journal that integration is now turned on for the journal. At this time:


 * 1) The journal sends notices to Dryad regarding manuscripts, and invites authors to deposit their data in Dryad.
 * 2) The journal is added to the list of Currently Integrated Journals on the Dryad website to enable prospective authors to see its settings and submit data at the appropriate time.
 * 3) The journal and Dryad may coordinate publicity on blogs etc., to announce the integration.
 * 4) The journal may wish to update their Instructions to Authors (see examples collected here, and announce the new data archiving process to authors.

Text of notifications Dryad sends to authors
These links point to email templates in Dryad's Github repository.


 * Submission received - article accepted (submission goes directly to curation)
 * Submission received - review
 * Rejection notification
 * Submission approved/archived publicly
 * Submission approved/archived but hidden until associated article is published (in "publication blackout")
 * Previously hidden submission now public (out of "publication blackout")

Ongoing integration
There are some related tasks that integrated journals should perform on an ongoing basis, once integration is implemented. These include:


 * Ensuring that authors follow the journal's data archiving policy (whether through deposit in Dryad or other repositories).
 * Ensuring that authors adequately cite data that is reused to produce results in an article.
 * Notifying Dryad when there are changes in the manuscript processing system that will affect metadata transfers.
 * Adding Dryad DOIs to online versions of articles in cases where authors have deposited data after article publication.

Documentation

 * Submission Integration: Overview
 * Submission Integration: Implementation (this page)
 * Journal Metadata -- details of metadata integrated journals should send to Dryad
 * Submission Integration: Current Status
 * Journal instructions -- elements of journal data policies, including data citation guidelines, and illustrative examples

Further resources

 * To begin the integration process, please review and complete: the Pre-Integration Questionnaire
 * Format specifications for automated email notices to Dryad: Journal Metadata
 * Sample text for email to authors inviting them to deposit data in Dryad
 * Submission process from a journal's perspective: Integration Overview Slides (PDF).
 * Blog post describing one journal's workflow for maximizing data archiving: How to decide what data should be archived at publication
 * Facilitating data publishing through journal integration: Poster PDF
 * Dryad is considering switching to a single standard integration workflow. View details and provide feedback. Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad and how we can work with you.