Submission Integration: Overview

What is submission 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. Journal integration with Dryad is available at no cost for any journal that wishes to implement low-burden data archiving and enhance their published articles with links to data. We invite journals to integrate their manuscript processing with Dryad for the benefit of their authors, regardless of their membership status in the Dryad organization.

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
 * enable editorial oversight of data and/or peer review of data, concurrent with manuscript review

Editors and publishers interested in implementing integration may review this documentation and [mailto:journalsetup@datadryad.org contact Dryad] or fill out the Pre-Integration Questionnaire to begin the integration process.

How it works
To make archiving as low-burden as possible for authors, data files are archived in conjunction with the journal’s manuscript submission process, resulting in permanent 2-way linking between an article and its data:


 * 1) Journal provides information about manuscripts to Dryad through automated notices from the manuscript processing system, which creates a provisional record for the data;
 * 2) Journal invites authors to archive data in Dryad, through a custom submission link that brings the author to the provisional record.
 * 3) Authors upload their files to Dryad through the submission link supplied by the journal; no redundant information need be entered and the article details are correct.
 * 4) Dryad Curators approve the data files and register its Digital Object Identifier (DOI), a permanent identifier that allows the data to be cited and tracked; curators convey the DOI to the journal.
 * 5) Journal and publisher add the Dryad DOI to all forms of the final article, enabling readers of the article to access the data.
 * 6) Dryad stores the data files, including spreadsheets, images, videos, audio recordings, and many other formats, and links to the article on the journal website. Dryad also provides links to data in other repositories, including sequences in GenBank and phylogenetic trees in TreeBASE.

Available options and customizations
Journals and publishers tell Dryad how they wish to configure integration to meet their needs. Journal editors maintain all communications with authors. Dryad staff only contact authors to approve their data deposits, convey the DOI, or handle questions.

These are some of the critical decisions and options for integrating journals:


 * to make data archiving voluntary, or a condition of publication
 * to request author permission before manuscript notifications are sent to Dryad
 * to allow or disallow authors' ability to set a one-year embargo for their data
 * to allow editors to establish custom-length embargoes in special cases
 * to offer anonymous and secure access to the data for editorial oversight or peer reviewers during the manuscript review process
 * to require Dryad to suppress all information about the article until it has been published
 * for journals that publish articles immediately upon acceptance, Dryad can provide a provisional DOI

Dryad staff are committed to ensuring that the integration process meets the needs of journals and publishers, and welcome suggestions for additional options and alternative workflows. Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad.

Documentation

 * Submission Integration: Ovreview (this page)
 * Submission Integration: Implementation
 * Submission Integration: Current Status

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 [[Media:Email_to_authors_INTEGRATED_JOURNALS.doc‎|email to authors]] inviting them to deposit data in Dryad
 * Submission process from a journal's perspective: [[Media:DryadIntegrationOverview.pdf|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

Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad and how we can work with you.

Proposed new consolidated workflow
The Dryad team is considering implementing some changes in early 2014 to the submission integration workflows to achieve a single standard workflow. Key points of this are:
 * enabling authors to deposit data to Dryad before submitting a manuscript,
 * allowing authors to deposit w/o having a custom link from the journal,
 * making optional the journal notice of a manuscript in review,
 * extending the benefits of the review workflow to all integrated journals.

Please add concerns on this page.

Here’s a summary of the new proposed workflow, with notes in bullets below each step. Add yours!


 * 1) Optional preliminary step: Journal notifies Dryad about a manuscript in review and invites the author to archive the underlying data files in Dryad, via a customized link.
 * 2) * Authors using the customized link won’t have to re-type information submitted to the journal.
 * 3) Author uploads data files to Dryad.
 * 4) * If no match on MS#, we need to display a note: We don't have any details about your article, so you will have to provide its description
 * 5) * change radio button In review to Prior to manuscript acceptance (?)
 * 6) * also need a radio button for "I don't have a MS#"
 * 7) Dryad sends immediate acknowledgement of data deposit w/ provisional DOI to author AND journal contacts ; sends reviewer passcode to journal contacts; also we state that we will not make this data public until we receive you final decision notice.
 * 8) * We will need to send these notices for every integrated journal, whether or not there has been a MS# match.
 * 9) * This is the first notice the journal gets w/ the Dryad DOI so it can be added to the article
 * 10) Journal contacts may access the data files using the passcode provided.
 * 11) At the conclusion of manuscript review, the journal notifies Dryad of accepted and rejected manuscripts. Should this be optional?
 * 12) * We would need to build the matching capability for this stage
 * 13) * Journals should send final decision notices for all accepted or rejected articles; they have no way to know which ones may have data in Dryad
 * 14) * there could payment consequences for journals that have a payment plan but don't want to pay for a data submission for whatever reason
 * 15) * if they don't send us a notice, spontaneously deposited data will sit in Review uncurated and the article could be published without the Dryad DOI; the journal has only received the immediate notice at the time of data deposit
 * 16) * Rejection notices are more valuable than acceptance; acceptance data can come from CrossRef
 * 17) Dryad matches the journal’s acceptance notice with the corresponding data files, OR curators use CrossRef checker to find published article; curators approve the data package and register the Digital Object Identifier (DOI); data files are hidden or made public per journal requirements.
 * 18) Journal and publisher add the Dryad DOI to all forms of the final article, enabling readers of the article to access the data.
 * 19) Dryad stores the data files, including spreadsheets, images, videos, audio recordings, and many other formats, and links to the article on the journal website.
 * 20) * Periodically we may need to contact both depositors & journals about data packages older than X? months for which we have not received an Acceptance notice.
 * 21) * Need periodic checker of submitted content to check on its status, send automated emails to author, possible automatic rejection after a timeout period

If adopted, these are some things that could require changes for our integrated journals:
 * some journals might not want to allow authors to deposit data before article acceptance; to know their preferences we would need to check in with each one
 * journals will need to send us acceptance notices for ALL manuscripts they handle, because they have no way of knowing which ones may have associated data being held in Dryad; otherwise the data will be held in limbo and unavailable
 * journals currently using the Basic workflow may need to change their workflow because this essentially forces them to be aware of data submitted during the ms review process, and they will not have a system in place for handling the reviewer passcode or any communications from Dryad before acceptance
 * curator reports might need to go to different people
 * weekly reports for journals now using the Basic workflow will look a little different
 * some journals might need to revise their Instructions to Authors