Difference between revisions of "Submission Integration: Implementation"

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== Overview of the review workflow ==
 
== Overview of the review workflow ==
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<gallery widths="200px">
 
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File:REVISEDSlide2.jpg|
 
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</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.
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.
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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.
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<li>Journal sends notice to the Dryad system for each submitted manuscript ([http://wiki.datadryad.org/Journal_Metadata see details]); Dryad creates a provisional record for the anticipated data.</li>
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<li>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.
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*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)
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*[http://wiki.datadryad.org/images/3/3b/Email_to_Authors-Dryad_Integrated_Journals.pdf sample text for use with authors]&nbsp;is available, describing the benefits of data deposit in Dryad
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*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</li>
  
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 retains the data in the authors' workspace for a year and it can be later associated with another journal.
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#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.
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#Dryad assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal, along with a temporary, secure review URL where journal reviewers and editors may access the data.
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#The journal either accepts or rejects the manuscript, and notifies both the author and Dryad of the decision.
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#*<span style="line-height: 18.9091px;"></span>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"
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#*<span style="line-height: 18.9091px;">the notice to Dryad and the notice to authors can be&nbsp;</span>'''combined into a single email'''<span style="line-height: 18.9091px;">&nbsp;that is sent to both parties</span>
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#If the MS is accepted, Dryad curators process and approve the data files and register the DOI. If it is rejected, the data package is returned to the submitter's personal workspace.
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#'''Journal includes the Dryad data reference with DOI in all print and online versions of published articles.'''
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#*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.
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#**suggested format for citation in article text:
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#***'''Data available from the Dryad Digital Repository:&nbsp;[http://doi.org/10.5061/dryad.j512f21p http://doi.org/10.5061/dryad.j512f21p]'''
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#**suggested format for citation in Reference list:
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#***'''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]'''
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#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.
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#Journal receives weekly reports from Dryad with DOIs for any new data submissions associated with its articles.
  
 
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 data review passcode. (This option does not the include first notice from the journal to Dryad, 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.
 
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 data review passcode. (This option does not the include first notice from the journal to Dryad, 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.

Revision as of 13:37, 10 November 2015

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. Journal sends notice to the Dryad system for each accepted manuscript (see details); 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.
  3. 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.
  4. Dryad curators review the data, performing basic checks on each file, and 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 weekly reports 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. 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. Journal sends notice to the Dryad system for each submitted manuscript (see details); 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.
    1. 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.
    2. Dryad assigns the data submission a Digital Object Identifier (DOI), which is sent to both the author and the journal, along with a temporary, secure review URL where journal reviewers and editors may access the data.
    3. The 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
    4. If the MS is accepted, Dryad curators process and approve the data files and register the DOI. If it is rejected, the data package is returned to the submitter's personal workspace.
    5. 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
    6. 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.
    7. Journal receives weekly reports from Dryad with DOIs for any new data submissions associated with its articles.
    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 data review passcode. (This option does not the include first notice from the journal to Dryad, 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.

    Implementation of review workflow using REST API and Dryad-first option

    For "Dryad-first":

    1. authors submit data packages as “in preparation or 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 (including DOI) and review link 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, including the Dryad DOI and/or review URL. 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).
      • In submit-to-dryad first, this needs to be review URL or DOI, which means this information must be included in the API call from the journal on acceptance/rejection
    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.

    Documentation

    Further resources

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