Difference between revisions of "Submission Integration: Implementation"

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(New page: The steps required to set up, test and roll out submission integration for a new journal are as follows: ===Initial Planning=== Journals initiating submission integration are welcome to [...)
 
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The steps required to set up, test and roll out submission integration for a new journal are as follows:
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The steps required to set up, test, roll out, and manage submission integration are described on this page.
  
===Initial Planning===
+
== Initial planning ==
Journals initiating submission integration are welcome to [mailto:help@datadryad.org contact Dryad staff] at any time to discuss the details of the process.  Some of the issues to discuss include:
 
* How the journal provides automated email notification to Dryad of new articles. Most journals opt to do this at the time of article acceptance.
 
* How the journal informs authors of the Dryad submission system URL.
 
* How Dryad will convey the data package DOI back to the journal.
 
* List of journal representatives that should receive reports from Dryad.
 
* Where the journal will publish the data DOIs.
 
* How Dryad will monitor the publication of accepted manuscripts (so Dryad curators can complete the bibliographic description).
 
* How to enable links to Dryad from publications.
 
* Whether/how to monitor or enforce timeliness of deposition.
 
* The timeline for the steps described below.
 
  
===Journal enables initial metadata transfer===
+
Journals initiating submission integration should [mailto:director@datadryad.org contact Dryad staff] to discuss the details of the process, and to fill out the [http://spreadsheets.google.com/viewform?hl=en&authkey=CKGswo8M&formkey=dC0yNlE4TDNPZU01R1FQM0FrS1BoM1E6MQ#gid=0 Pre-Integration Questionnaire]. Some of the issues to discuss include:
# The email from the journal contains basic bibliographic information about each article, generally at the time of acceptance (see [[Journal Metadata|the detailed email format]])
 
# If you use ScholarOne Manuscripts (Manuscript Central) for processing manuscripts, you can implement the [[Media:DryadSetupForMC-TimVines.pdf‎|Manuscript Central template for Dryad]] created by Tim Vines. Another [[Media:SeekAuthorConsentFirstREV2.pdf|document]] describes an additional process to seek author consent before sending manuscript details to Dryad.
 
# If you have another manuscript tracking system, an equivalent email template will need to be created. Dryad staff can assist with this.
 
  
===Testing of metadata transfer for new articles===
+
*Summarize workflow options, confirm journal preferences (embargoes, data available during the review process, etc.)
# The journal begins sending new article metadata and Dryad begins creating new records in a testing environment.
+
*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.
# Dryad staff and journal representatives test the submission system, specifically the integrity of the metadata transfer.
+
*How the journal will invite authors to deposit data, and provide the Dryad submission system URL.
# Any problems that are discovered are resolved, and testing is repeated until no more issues are found.
+
*Where the journal will include the Dryad DOI in the published articles.
# Dryad and/or journal representatives ask a few authors to test the system in the production environment.
+
*Whether/how the journal will monitor or enforce timeliness of deposition.
# Any problems that are discovered are resolved, and testing is repeated until no more issues are found.
+
*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.
  
===Testing Dryad's ability to extract metadata at the time of publication===
+
== Overview of the basic workflow: data submission after article acceptance ==
# Journal provides additional metadata about each published article.
 
# Dryad tests ability to retrieve necessary information, and iterates until all issues are resolved.
 
# This can be done in parallel with the above steps.
 
  
===Rollout to authors===
+
<gallery widths="200px">
# Journal provides Dryad submission system URLs to all acceptance letters, asking authors to voluntarily submit data.
+
File:NEWSlide1.jpg|
# Dryad provides journal with list of all pre-existing identifiers for the journal's articles in Dryad.
+
</gallery>
# Dryad begins to send identifiers to journal as new datasets are deposited. (Description of first quarter 2010 reporting practices: [[Media:January2010ReportingPractices.pdf|PDF]], [[Media:January2010ReportingPractices.doc|Word]])
 
# Journal includes identifiers within print and online versions of published articles. (A sample placement of the DOI can be seen on the front page of this [http://dx.doi.org/doi:10.1086/652994 article by Fuller et al., in The American Naturalist].)
 
# Dryad will provide any information the journal may need to verify deposits, but enforcement of deposition policy is the responsibility of the journal.
 
# The journal may choose to announce the rollout to its authors.
 
  
[[Category:Submission Integration]]
+
#<span style="color:#0000FF;">'''Author'''</span> submits manuscript to journal.
[[Category:Journals]]
+
#<span style="color:#800080;">'''Journal'''</span> sends notice to the Dryad system for each ''accepted'' manuscript ([http://wiki.datadryad.org/Journal_Metadata see details]); <span style="color:#008000;">'''Dryad'''</span> uses it to create a provisional record for the anticipated data.
 +
#<span style="color:#800080;">'''Journal'''</span> 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.
 +
#*format for the submission link to Dryad:&nbsp;'''[http://datadryad.org/submit?journalID=ABCD&manu=NNNN 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)
 +
#*[http://wiki.datadryad.org/images/3/3b/Email_to_Authors-Dryad_Integrated_Journals.pdf sample text for use with authors] is available, describing the benefits of data deposit in Dryad
 +
#*note that the notice to Dryad and the notice to authors can be '''combined into a single email''' that is sent to both parties
 +
#<span style="color:#0000FF;">'''Author'''</span> uses the custom link to access the provisional Dryad record (with manuscript info pre-filled), uploads data files, and submits data package to Dryad.
 +
#<span style="color: rgb(0, 128, 0);">'''Dryad'''</span>&nbsp;assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal immediately upon submission ([https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_confirm see email template]).
 +
#<span style="color:#008000;">'''Dryad'''</span> curators review the data, performing basic checks on each file, and approve the release of the data package.
 +
#<span style="color:#800080;">'''Journal'''</span> includes the Dryad data reference with DOI in all print and online versions of published articles.
 +
#*Dryad suggests, following [http://www.crossref.org/10quarterly/quarterly_jan12.html#dois_in_use CrossRef] and [http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/ 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.
 +
#**suggested format for citation in article text:
 +
#***'''Data available from the Dryad Digital Repository: [http://doi.org/10.5061/dryad.j512f21p http://doi.org/10.5061/dryad.j512f21p]'''
 +
#**suggested format for citation in Reference list:
 +
#***'''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 http://doi.org/10.5061/dryad.t903h]'''
 +
#<span style="color:#008000;">'''Dryad'''</span> 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.
 +
#<span style="color:#008000;">'''Dryad'''</span> sends the journal weekly reports with DOIs for any new data submissions associated with its articles.
 +
 
 +
== Overview of the review workflow ==
 +
 
 +
<gallery widths="200px">
 +
File:REVISEDSlide2.jpg|
 +
</gallery> 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.
 +
 
 +
#<span style="color: rgb(0, 0, 255);">'''Author'''</span>&nbsp;submits manuscript to journal.
 +
#<span style="color:#800080;">'''Journal'''</span> sends notice to the Dryad system for all&nbsp;''submitted'' manuscripts ([http://wiki.datadryad.org/Journal_Metadata see details]); <span style="color:#008000;">'''Dryad'''</span> creates a provisional record for the anticipated data.
 +
#<span style="color:#800080;">'''Journal'''</span> 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.
 +
#*format for the submission link to Dryad:&nbsp;'''[http://datadryad.org/submit?journalID=ABCD&manu=NNNN http://datadryad.org/submit?journalID=ABCD&amp;manu=NNNN]'''&nbsp;(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)
 +
#*[http://wiki.datadryad.org/images/a/ab/EmailToAuthorsForIntegratedJournals.pdf sample text for use with authors]&nbsp;is available, describing the benefits of data deposit in Dryad
 +
#*note that the notice to Dryad and the notice to authors can be&nbsp;'''combined into a single email'''&nbsp;that is sent to both parties
 +
#<span style="color:#0000FF;">'''Author'''</span> uses the custom link to access the provisional Dryad record (with manuscript info pre-filled), uploads data files, and submits data package to Dryad.
 +
#<span style="color:#008000;">'''Dryad'''</span> assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal <span style="line-height: 20.8px;">immediately upon submission</span>, along with a temporary, secure review URL where journal reviewers and editors may access the data ([https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_review see email template]).
 +
#<span style="color:#800080;">'''Journal'''</span> either accepts or rejects the manuscript, and notifies both the author and Dryad of the decision.
 +
#*the second notice includes the same fields as the first one ([http://wiki.datadryad.org/Journal_Metadata see details]<span style="line-height: 18.9091px;">), but&nbsp;</span>with Article Status: either "accepted" or "rejected"
 +
#*the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
 +
#<span style="color:#008000;">'''Dryad'''</span> curators process and approve the data files and register the DOI if the MS is accepted ([https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_archive see notification email template]).
 +
#*If the MS or data package is rejected, the submission is returned to the submitter's personal workspace ([https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_reject see notification email template]).
 +
#<span style="color:#800080;">'''Journal'''</span> includes the Dryad data reference with DOI in all print and online versions of published articles.
 +
#*Dryad suggests, following&nbsp;[http://www.crossref.org/10quarterly/quarterly_jan12.html#dois_in_use CrossRef]&nbsp;and&nbsp;[http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/ BioMed Central]&nbsp;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.
 +
#**suggested format for citation in article text:
 +
#***'''Data available from the Dryad Digital Repository:&nbsp;[http://doi.org/10.5061/dryad.j512f21p http://doi.org/10.5061/dryad.j512f21p]'''
 +
#**suggested format for citation in Reference list:
 +
#***'''Sadd BM (2011) Data from: Food-environment mediates the outcome of specific interactions between a bumblebee and its trypanosome parasite. Dryad Digital Repository.&nbsp;[http://doi.org/10.5061/dryad.t903h http://doi.org/10.5061/dryad.t903h]'''
 +
#<span style="color:#008000;">'''Dryad'''</span> 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.
 +
#<span style="color:#008000;">'''Dryad'''</span> 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 [http://wiki.datadryad.org/Dryad_REST_API_Technology#Implementation_of_review_workflow_using_REST_API_and_Dryad-first_option 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:
 +
 
 +
#The journal sends several test article notifications, and Dryad creates new records in a testing environment.
 +
#*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.
 +
#Dryad staff and journal representatives test the notifications, specifically the integrity of the information transfer to Dryad.
 +
#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:
 +
 
 +
#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.
 +
#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 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 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:
 +
 
 +
#The journal sends notices to Dryad regarding manuscripts, and invites authors to deposit their data in Dryad.
 +
#The journal is added to the list of [http://datadryad.org/pages/integratedJournals Currently Integrated Journals] on the Dryad website to enable prospective authors to see its settings and submit data at the appropriate time.
 +
#The journal and Dryad may coordinate publicity on blogs etc., to announce the integration.
 +
#The journal may wish to update their Instructions to Authors (see examples collected [http://wiki.datadryad.org/Journal_instructions 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.
 +
 
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_confirm Submission received - article accepted] (submission goes directly to curation)
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_review Submission received - review]
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_reject Rejection notification]
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_archive Submission approved/archived publicly]
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_blackout Submission approved/archived but hidden until associated article is published]&nbsp;(in "publication blackout")
 +
*[https://github.com/datadryad/dryad-repo/blob/dryad-master/dspace/config/emails/submit_datapackage_blackout_archive Previously hidden submission now public]&nbsp;(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: [http://spreadsheets.google.com/viewform?hl=en&authkey=CKGswo8M&formkey=dC0yNlE4TDNPZU01R1FQM0FrS1BoM1E6MQ#gid=0 the Pre-Integration Questionnaire]
 +
*Format specifications for automated email notices to Dryad: [[Journal Metadata]]
 +
*Sample text for [http://wiki.datadryad.org/images/a/ab/EmailToAuthorsForIntegratedJournals.pdf email to authors] inviting them to deposit data in Dryad
 +
*Submission process from a journal's perspective: [http://wiki.datadryad.org/images/c/c6/DryadIntegrationOverview.pdf Integration Overview Slides (PDF)].
 +
*Blog post describing one journal's workflow for maximizing data archiving: [http://blog.datadryad.org/2013/02/02/how-to-decide-what-data-should-be-archived-at-publication/ How to decide what data should be archived at publication]
 +
*Facilitating data publishing through journal integration:&nbsp;[http://wiki.datadryad.org/images/0/06/Hull-RDA_2015_poster.pdf Poster PDF]
 +
*Dryad is considering switching to a single standard integration workflow. [[Submission Integration: Proposed Consolidated 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.'''

Latest revision as of 08:28, 31 May 2017

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 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.
    • format for the submission link to Dryad: http://datadryad.org/submit?journalID=ABCD&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)
    • sample text for use with authors is available, describing the benefits of data deposit in Dryad
    • note that the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
  4. 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.
  5. 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).
  6. Dryad curators review the data, performing basic checks on each file, and approve the release of the data package.
  7. Journal includes the Dryad data reference with DOI in all print and online versions of published articles.
    • 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.
      • suggested format for citation in article text:
      • suggested format for citation in Reference list:
        • 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
  8. 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.
  9. 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.
    • format for the submission link to Dryad: http://datadryad.org/submit?journalID=ABCD&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)
    • sample text for use with authors is available, describing the benefits of data deposit in Dryad
    • note that the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
  4. 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.
  5. 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).
  6. Journal either accepts or rejects the manuscript, and notifies both the author and Dryad of the decision.
    • the second notice includes the same fields as the first one (see details), but with Article Status: either "accepted" or "rejected"
    • the notice to Dryad and the notice to authors can be combined into a single email that is sent to both parties
  7. Dryad curators process and approve the data files and register the DOI if the MS is accepted (see notification email template).
  8. Journal includes the Dryad data reference with DOI in all print and online versions of published articles.
    • 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.
      • suggested format for citation in article text:
      • suggested format for citation in Reference list:
        • 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
  9. 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.
  10. 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 contact us to discuss the details.

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.
    • 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.
  2. Dryad staff and journal representatives test the notifications, specifically the integrity of the information transfer to Dryad.
  3. 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.

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

Further resources