Difference between revisions of "Submission Integration: Implementation"

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m (Overview of the Review workflow using REST API)
(moved "proposed consolidated workflow" section here)
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*Where the journal will include the Dryad DOI in the published articles.
 
*Where the journal will include the Dryad DOI in the published articles.
 
*Whether/how the journal will monitor or enforce timeliness of deposition.
 
*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.<br>
+
*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).
 
*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.
 
*The timeline for testing the process and for implementation with authors.
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=== Overview of the basic workflow ===
 
=== Overview of the basic workflow ===
  
# Journal sends notice to the Dryad system for each accepted manuscript; Dryad creates a provisional record for the anticipated data.
+
#Journal sends notice to the Dryad system for each accepted manuscript; Dryad creates a provisional record for the anticipated data.
# 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.
+
#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:
 
#*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)
+
#**'''[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)
#*sample text for use with authors is available, describing the benefits of data deposit in Dryad, [[Media:Email_to_authors_INTEGRATED_JOURNALS.doc‎|here]].
+
#*sample text for use with authors is available, describing the benefits of data deposit in Dryad, [[/wg/dryad/images/e/e8/Email_to_authors_INTEGRATED_JOURNALS.doc|here]].
# Author uses the custom link to access the provisional Dryad record, and uploads data.
+
#Author uses the custom link to access the provisional Dryad record, and uploads data.
# Dryad curators review the data, performing basic checks on each file, then approve the release of the data package.
+
#Dryad curators review the data, performing basic checks on each file, then approve the release of the data package.
# Dryad notifies the journal of each new data deposit associated with the journal, and its DOI.
+
#Dryad notifies the journal of each new data deposit associated with the journal, and its DOI.
# '''Journal includes the Dryad data reference with DOI in all print and online versions of published articles.'''
+
#'''Journal 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 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.
+
#*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 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 article text:
#***'''Data available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.j512f21p'''
+
#***'''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:
+
#**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'''
+
#***'''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]'''
# 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.
+
#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.
# Journal receives reports (usually weekly) from Dryad with DOIs for any new data submissions associated with its articles
+
#Journal receives reports (usually weekly) from Dryad with DOIs for any new data submissions associated with its articles
  
 
=== Overview of the review workflow ===
 
=== 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. This workflow is the same as the basic workflow, except that data files are submitted to Dryad while the manuscript is in review. Journals using the review workflow receive a passcode enabling private access to the data. Authors can add new versions of files to respond to editorial or reviewers' concerns.
+
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. This workflow is the same as the basic workflow, except that data files are submitted to Dryad while the manuscript is in review. Journals using the review workflow receive a passcode enabling private access to the data. Authors can add new versions of files to respond to editorial or reviewers' concerns.
  
 
Journals using the review workflow '''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 retains the data in the authors' workspace for a year and it can be later associated with another journal.
 
Journals using the review workflow '''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 retains the data in the authors' workspace for a year and it can be later associated with another journal.
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For Submit to Dryad first:
 
For Submit to Dryad first:
  
# authors submit data packages as “in review” and don’t enter a manuscript number (they won’t have one yet)
+
#authors submit data packages as “in review” and don’t enter a manuscript number (they won’t have one yet)
# data packages go to review (still have no manuscript number). Dryad sends review emails and links to author and to journal
+
#data packages go to review (still have no manuscript number). Dryad sends review emails and links to author and to journal
# author submits manuscript to journal, including the Dryad DOI and/or review link
+
#author submits manuscript to journal, including the Dryad DOI and/or review link
# Journal sends API calls to Dryad on acceptance/rejection. Generally works like the email system - they specify a journal code (organization code) and a structured JSON object containing manuscript metadata
+
#Journal sends API calls to Dryad on acceptance/rejection. Generally works like the email system - they specify a journal code (organization code) and a structured JSON object containing manuscript metadata
#* Examples here: [[Journal_Metadata#Metadata_Submission_via_API|Metadata Submission via API]]
+
#*Examples here: [[Journal Metadata#Metadata Submission via API|Metadata Submission via API]]
# API finds the data package that matches the incoming manuscript metadata (it looks it up by review URL, DOI, or manuscript number).
+
#API finds the data package that matches the incoming manuscript metadata (it looks it up by review URL, DOI, or manuscript number).
## In submit-to-dryad first, this needs to be review URL or DOI.
+
##In submit-to-dryad first, this needs to be review URL or DOI.
# API approves the submission from review to curation (when the status is “accepted”) and synchronizes the following metadata fields
+
#API approves the submission from review to curation (when the status is “accepted”) and synchronizes the following metadata fields
## Publication DOI
+
##Publication DOI
## Manuscript Number
+
##Manuscript Number
## Keywords
+
##Keywords
## Title (takes the title and prefixes it with “Data from: “
+
##Title (takes the title and prefixes it with “Data from: “
## Abstract
+
##Abstract
## Blackout until date aka publication date
+
##Blackout until date aka publication date
  
 
Some other things to note:
 
Some other things to note:
  
# When we receive API calls we will probably not be receiving metadata emails. The JSON data is protected with OAuth, and we can grant access to Dryad personnel.
+
#When we receive API calls we will probably not be receiving metadata emails. The JSON data is protected with OAuth, and we can grant access to Dryad personnel.
# The API will store the received JSON data in the database, but it will also make XML files just like the email system does - so these can be checked too. This supports the submit-to-journal first case
+
#The API will store the received JSON data in the database, but it will also make XML files just like the email system does - so these can be checked too. This supports the submit-to-journal first case
# We’re recording the publication date in the dc.date.blackoutUntil field (new field!). This date will be used to automatically publish things from blackout but this part is not yet functional.
+
#We’re recording the publication date in the dc.date.blackoutUntil field (new field!). This date will be used to automatically publish things from blackout but this part is not yet functional.
# If the metadata sent by the journal is invalid or doesn’t match a data package in review, the API won’t be able to find the data package and it will stay in review. Something to be aware of.
+
#If the metadata sent by the journal is invalid or doesn’t match a data package in review, the API won’t be able to find the data package and it will stay in review. Something to be aware of.
  
===Testing the format of journal notices ===
+
=== 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.
 
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.
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This is the testing process:
 
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.
+
#The journal sends several test article notifications, and Dryad creates new records in a testing environment.
# Dryad staff and journal representatives test the notifications, specifically the integrity of the information transfer to Dryad.
+
#*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.
# Any problems that are discovered are resolved, and testing is repeated until no more issues are found.
+
#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.
  
 
During the test phase, journals should use the [http://staging.datadryad.org/ Dryad staging server] to test and see how data submissions are handled. Journal staff can use this server for any end-to-end tests they wish to conduct, can create accounts, and upload data files.
 
During the test phase, journals should use the [http://staging.datadryad.org/ Dryad staging server] to test and see how data submissions are handled. Journal staff can use this server for any end-to-end tests they wish to conduct, can create accounts, and upload data files.
  
===Implementation of integration and rollout to authors ===
+
=== 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:
+
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 sends notices to Dryad regarding manuscripts, and invites authors to deposit their data in Dryad.
# The journal and Dryad may coordinate publicity on blogs etc., to announce the integration.
+
#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 may wish to update their Instructions to Authors (see examples collected [http://www.nescent.org/wg_dryad/Journal_instructions here], and announce the new data archiving process to authors.
+
#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://www.nescent.org/wg_dryad/Journal_instructions here], and announce the new data archiving process to authors.
  
 
=== Ongoing integration ===
 
=== Ongoing integration ===
  
 
There are some related tasks that integrated journals should perform on an ongoing basis, once integration is implemented. These include:
 
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.
+
*Ensuring that authors follow the journal's data archiving policy (whether through deposit in Dryad or other repositories).
* Notifying Dryad when there are changes in the manuscript processing system that will affect metadata transfers.
+
*Ensuring that authors adequately cite data that is reused to produce results in an article.
* Adding Dryad DOIs to online versions of articles in cases where authors have deposited data after article publication.
+
*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.
 +
 
 +
=== Proposed new consolidated workflow ===
 +
 
 +
The Dryad team is considering implementing some changes to the submission integration workflows to achieve a single standard workflow. Key points of this are:
 +
<ul style="font-size: 11.8181819915771px;">
 +
<li>enabling authors to deposit data to Dryad before submitting a manuscript,</li>
 +
<li>allowing authors to deposit w/o having a custom link from the journal,</li>
 +
<li>making optional the journal notice of a manuscript in review,</li>
 +
<li>extending the benefits of the review workflow to all integrated journals.</li>
 +
</ul>
 +
 
 +
Please add concerns on this page.
 +
<ul style="font-size: 11.8181819915771px;">
 +
<li>increased use of the review option as it's currently implemented will result in more duplicate submissions, and thus more journal and curator time spent sorting them out. authors are unsure of what they can and cannot do while their submissions are in review, and when things don't go as they expect, they often start over with a new submission.</li>
 +
</ul>
 +
 
 +
Here’s a summary of the new proposed workflow, with notes in bullets below each step. Add yours!
 +
<ol style="font-size: 11.8181819915771px;">
 +
<li>''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.
 +
*Authors using the customized link won’t have to re-type information submitted to the journal.</li>
 +
 
 +
#Author uploads data files to Dryad.
 +
#*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
 +
#*change radio button&nbsp;''In review''&nbsp;to&nbsp;''Prior to manuscript acceptance''&nbsp;(?)
 +
#*also need a radio button for "I don't have a MS#"
 +
#Dryad sends immediate acknowledgement of data deposit w/ provisional DOI to author AND journal contacts&nbsp;; sends reviewer passcode to journal contacts; also we state that we will not make this data public until we receive you final decision notice.
 +
#*We will need to send these notices for every integrated journal, whether or not there has been a MS# match.
 +
#*This is the first notice the journal gets w/ the Dryad DOI so it can be added to the article
 +
#Journal contacts may access the data files using the passcode provided.
 +
#At the conclusion of manuscript review, the journal notifies Dryad of accepted and rejected manuscripts.&nbsp;''Should this be optional?''
 +
#*We would need to build the matching capability for this stage
 +
#*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
 +
#*there could payment consequences for journals that have a payment plan but don't want to pay for a data submission for whatever reason
 +
#*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
 +
#*Rejection notices are more valuable than acceptance; acceptance data can come from CrossRef
 +
#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.
 +
#Journal and publisher add the Dryad DOI to all forms of the final article, enabling readers of the article to access the data.
 +
#Dryad stores the data files, including spreadsheets, images, videos, audio recordings, and many other formats, and links to the article on the journal website.
 +
#*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.
 +
#*Need periodic checker of submitted content to check on its status, send automated emails to author, possible automatic rejection after a timeout period
 +
 
 +
<br/>If adopted, these are some things that could require changes for our integrated journals:
 +
<ul style="font-size: 11.8181819915771px;">
 +
<li>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</li>
 +
<li>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</li>
 +
<li>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</li>
 +
<li>curator reports might need to go to different people</li>
 +
<li>weekly reports for journals now using the Basic workflow will look a little different</li>
 +
<li>some journals might need to revise their Instructions to Authors</li>
 +
</ul>
  
 
== Documentation ==
 
== Documentation ==
* [[Submission Integration: Overview]]
+
 
* [[Submission Integration: Implementation]] (this page)
+
*[[Submission Integration: Overview]]
* [[Submission Integration: Current Status]]
+
*'''RTENOTITLE''' (this page)
 +
*[[Submission Integration: Current Status]]
  
 
== Further resources ==
 
== Further resources ==
* To begin the integration process, please review and complete: [http://spreadsheets.google.com/viewform?hl=en&amp;authkey=CKGswo8M&amp;formkey=dC0yNlE4TDNPZU01R1FQM0FrS1BoM1E6MQ#gid=0 the Pre-Integration Questionnaire]
+
 
* Format specifications for automated email notices to Dryad: [[Journal Metadata]]
+
*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]
* Sample text for [[Media:Email_to_authors_INTEGRATED_JOURNALS.doc‎|email to authors]] inviting them to deposit data in Dryad
+
*Format specifications for automated email notices to Dryad: [[Journal Metadata]]
* Submission process from a journal's perspective: [[Media:DryadIntegrationOverview.pdf|Integration Overview Slides (PDF)]].
+
*Sample text for [[/wg/dryad/images/e/e8/Email_to_authors_INTEGRATED_JOURNALS.doc|email to authors]] inviting them to deposit data in Dryad
* 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]
+
*Submission process from a journal's perspective: [[/wg/dryad/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]
  
 
Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad and how we can work with you.
 
Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad and how we can work with you.
 
[[Category:Submission Integration]]
 
[[Category:Journals]]
 

Revision as of 11:20, 5 December 2014

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

  1. Journal sends notice to the Dryad system for each accepted manuscript; Dryad creates a provisional record for the anticipated data.
  2. 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:
    • sample text for use with authors is available, describing the benefits of data deposit in Dryad, here.
  3. Author uses the custom link to access the provisional Dryad record, and uploads data.
  4. Dryad curators review the data, performing basic checks on each file, then approve the release of the data package.
  5. Dryad notifies the journal of each new data deposit associated with the journal, and its DOI.
  6. 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
  7. 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.
  8. Journal receives reports (usually weekly) from Dryad 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. This workflow is the same as the basic workflow, except that data files are submitted to Dryad while the manuscript is in review. Journals using the review workflow receive a passcode enabling private access to the data. Authors can add new versions of files to respond to editorial or reviewers' concerns.

Journals using the review workflow 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 retains the data in the authors' workspace for a year and it can be later associated with another journal.

Overview of the review workflow using REST API

Currently under initial roll-out. This workflow supports two options - submit to Dryad first or submit to Journal first.

For Submit to Dryad first:

  1. authors submit data packages as “in review” and don’t enter a manuscript number (they won’t have one yet)
  2. data packages go to review (still have no manuscript number). Dryad sends review emails and links to author and to journal
  3. author submits manuscript to journal, including the Dryad DOI and/or review link
  4. Journal sends API calls to Dryad on acceptance/rejection. Generally works like the email system - they specify a journal code (organization code) and a structured JSON object containing manuscript metadata
  5. API finds the data package that matches the incoming manuscript metadata (it looks it up by review URL, DOI, or manuscript number).
    1. In submit-to-dryad first, this needs to be review URL or DOI.
  6. API approves the submission from review to curation (when the status is “accepted”) and synchronizes the following metadata fields
    1. Publication DOI
    2. Manuscript Number
    3. Keywords
    4. Title (takes the title and prefixes it with “Data from: “
    5. Abstract
    6. Blackout until date aka publication date

Some other things to note:

  1. When we receive API calls we will probably not be receiving metadata emails. The JSON data is protected with OAuth, and we can grant access to Dryad personnel.
  2. The API will store the received JSON data in the database, but it will also make XML files just like the email system does - so these can be checked too. This supports the submit-to-journal first case
  3. We’re recording the publication date in the dc.date.blackoutUntil field (new field!). This date will be used to automatically publish things from blackout but this part is not yet functional.
  4. If the metadata sent by the journal is invalid or doesn’t match a data package in review, the API won’t be able to find the data package and it will stay in review. Something to be aware of.

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.

During the test phase, journals should use the Dryad staging server to test and see how data submissions are handled. Journal staff can use this server for any end-to-end tests they wish to conduct, can create accounts, and upload data files.

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.

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.

Proposed new consolidated workflow

The Dryad team is considering implementing some changes 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.

  • increased use of the review option as it's currently implemented will result in more duplicate submissions, and thus more journal and curator time spent sorting them out. authors are unsure of what they can and cannot do while their submissions are in review, and when things don't go as they expect, they often start over with a new submission.

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.
    • Authors using the customized link won’t have to re-type information submitted to the journal.
    1. Author uploads data files to Dryad.
      • 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
      • change radio button In review to Prior to manuscript acceptance (?)
      • also need a radio button for "I don't have a MS#"
    2. 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.
      • We will need to send these notices for every integrated journal, whether or not there has been a MS# match.
      • This is the first notice the journal gets w/ the Dryad DOI so it can be added to the article
    3. Journal contacts may access the data files using the passcode provided.
    4. At the conclusion of manuscript review, the journal notifies Dryad of accepted and rejected manuscripts. Should this be optional?
      • We would need to build the matching capability for this stage
      • 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
      • there could payment consequences for journals that have a payment plan but don't want to pay for a data submission for whatever reason
      • 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
      • Rejection notices are more valuable than acceptance; acceptance data can come from CrossRef
    5. 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.
    6. Journal and publisher add the Dryad DOI to all forms of the final article, enabling readers of the article to access the data.
    7. Dryad stores the data files, including spreadsheets, images, videos, audio recordings, and many other formats, and links to the article on the journal website.
      • 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.
      • 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

    Documentation

    Further resources

    Please contact Dryad to let us know your questions about integration with Dryad and how we can work with you.