Difference between revisions of "Submission Integration: Overview"

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== What is submission integration with Dryad? ==
 
== What is submission integration with Dryad? ==
  
Integration with Dryad allows journals to facilitate data archiving by setting up automatic notifications to Dryad from the journals' manuscript submission system. '''Journal integration with Dryad is available at no cost for any journal that wishes to implement low-burden data archiving and enhance their published articles with links to data.''' We invite journals to integrate their manuscript processing with Dryad for the benefit of their authors, regardless of their membership status in the Dryad organization.
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Integration with Dryad allows journals to facilitate data archiving by setting up automatic communications between journals and Dryad. Journal integration with Dryad is '''available at no cost for any journal '''that wishes to implement low-burden data archiving and enhance their published articles with links to data'''.'''
 +
 
 +
We invite journals to integrate their manuscript processing with Dryad for the benefit of their authors, regardless of their membership status in the Dryad organization.
  
 
Advantages of integration include:
 
Advantages of integration include:
  
*streamlining the authors’ data deposit process
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*'''streamlining''' the authors’ data deposit process
*permanently linking the published article with its securely archived data
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*permanently '''linking''' the published article with its securely archived data
*allowing authors to deposit complex and varied data types in robust re-usable formats
+
*'''enhancing visibility''' of the article via linking from the data package
*ensuring that data files are discoverable, indexed, and exposed to both web and bibliographic search engines
+
*allowing authors to deposit '''complex and varied data types''' in robust re-usable formats
*enhancing visibility of the article via linking from the data files
+
*ensuring that data files are '''discoverable''', indexed, and exposed to both web and bibliographic search engines
*permitting embargoes to delay release of data, in accordance with journal policy
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*permitting '''embargoes''' to delay release of data, in accordance with journal policy
*enable editorial oversight of data and/or peer review of data, concurrent with manuscript review
+
*enable editorial oversight of data and/or '''peer review of data''', concurrent with manuscript review
  
Editors and publishers interested in implementing integration may review this documentation and [mailto:journalsetup@datadryad.org contact Dryad] or fill out the [http://spreadsheets.google.com/viewform?hl=en&authkey=CKGswo8M&formkey=dC0yNlE4TDNPZU01R1FQM0FrS1BoM1E6MQ#gid=0 Pre-Integration Questionnaire] to begin the integration process.
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Editors and publishers interested in implementing integration may review this documentation and [mailto:director@datadryad.org contact Dryad] or fill out the [http://spreadsheets.google.com/viewform?hl=en&authkey=CKGswo8M&formkey=dC0yNlE4TDNPZU01R1FQM0FrS1BoM1E6MQ#gid=0 Pre-Integration Questionnaire] to begin the integration process.
  
 
== How it works ==
 
== How it works ==
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#Authors submit their manuscripts to the journal for consideration.
 
#Authors submit their manuscripts to the journal for consideration.
 
#Journal provides information about manuscripts to Dryad through automated notices from the manuscript processing system, which creates a provisional Dryad record for the data.
 
#Journal provides information about manuscripts to Dryad through automated notices from the manuscript processing system, which creates a provisional Dryad record for the data.
#Journal invites authors to archive data in Dryad, through a custom submission link that brings the author to the provisional record.
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#Journal invites authors to archive data in Dryad, providing them a custom submission link that brings the author to the provisional record.
#Authors upload their files to Dryad through the submission link supplied by the journal; no redundant information need be entered and the article details are correct.
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#Authors upload their files to Dryad using the submission link supplied by the journal; no redundant information need be entered and the article details are correct. T<span style="line-height: 18.9091px;">he submission is assigned a Digital Object Identifier (DOI), which is sent to both the author and the journal.</span>
#Dryad Curators process and approve the data files and register the Digital Object Identifier (DOI), a permanent identifier that allows the data to be cited and tracked; curators convey the DOI to the journal.
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#Dryad curators process and approve the data files and register the DOI.
 
#Journal and publisher add the Dryad DOI to all forms of the final article, enabling readers of the article to access the data.
 
#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. Dryad can also provide links to data in other repositories, including sequences in GenBank and phylogenetic trees in TreeBASE.
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#Dryad stores the data files (including spreadsheets, images, videos, audio recordings, and many other formats) and links the data package back to the journal article. Dryad can also provide links to data in other repositories, including sequences in GenBank and phylogenetic trees in TreeBASE.
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 +
<span style="color: rgb(0, 0, 0); font-family: sans-serif; font-size: 12.7px; line-height: 19.05px;">The steps required to set up, test, roll out, and manage submission integration are described on the [http://wiki.datadryad.org/Submission_Integration:_Implementation Implementation] page.</span>
  
 
== Available options and customizations ==
 
== Available options and customizations ==
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These are some of the critical questions for integrating journals:
 
These are some of the critical questions for integrating journals:
  
*is data archiving voluntary or required?
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*Is data archiving voluntary or required?
*does the journal want to have (secure) access to the data during manuscript review?
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*Does the journal want to have (secure) access to the data during manuscript review?
*are articles published immediately upon acceptance (necessitating a provisional Dryad DOI)?
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**''learn more about the [http://wiki.datadryad.org/Submission_Integration:_Implementation#Overview_of_the_review_workflow review workflow]''
*should authors be able to set a one-year embargo for their data?
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*Should the data be accessible in Dryad ''before'' the manuscript is submitted?
*should editors be able to set custom-length data embargoes (in special cases)?
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**''learn more about the [http://wiki.datadryad.org/Submission_Integration:_Implementation#Dryad-first_option Dryad-first option]''
*should Dryad suppress all information about the article until it has been published?
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*Should authors be able to set a one-year embargo for their data?
*is author permission needed before manuscript notifications are sent to Dryad?
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*Should editors be able to set custom-length data embargoes (in special cases)?
 +
*At what point in the article publication process should the data be made available on the Dryad website?
 +
**''learn more about [http://wiki.datadryad.org/Submission_Integration:_Implementation#Timing_of_data_release timing of data release]''
 +
*Will the journal, publisher, or society sponsor&nbsp;Dryad's Data Publishing Charges on behalf of their authors?
 +
**''learn more about our discounted [http://datadryad.org/pages/payment payment plans]''
  
Dryad supports '''multiple ways of receiving article or manuscript metadata from publishers'''. The simplest method involves reading email notifications, but we are also implementing a [[Journal Metadata#Metadata Submission via API|REST API]] for those desiring greater control over the data deposition process.
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Dryad supports '''multiple ways of receiving article or manuscript metadata from publishers'''. The simplest method involves reading email notifications, but we are also implementing a [http://wiki.datadryad.org/Journal_Metadata#Metadata_Submission_via_REST_API REST API] for those desiring greater control over the data deposition process.
 
 
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 with their MS submission. (This option does not include the benefit of the provisional Dryad record or the custom journal invitation/submission link, meaning that authors must provide information about their MS to Dryad manually).
 
 
 
'''Dryad staff are committed to ensuring that the integration process meets the needs of journals and publishers, and welcome suggestions for additional options and alternative workflows. Please [mailto:journalsetup@datadryad.org contact Dryad] to let us know your questions about integration with Dryad.'''
 
 
 
=== 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.
 
*One concern is that 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!
 
*''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.
 
**Benefit: authors using the customized link won’t have to re-type information submitted to the journal.
 
#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
 
  
If adopted, these are some things that could require changes for our integrated journals:
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'''Dryad staff are committed to ensuring that the integration process meets the needs of journals and publishers, and welcome suggestions for additional options and alternative workflows. Please [mailto:director@datadryad.org contact Dryad] to let us know your questions about integration with Dryad.'''
*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 ==
 
== Documentation ==
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*[[Submission Integration: Implementation]]&nbsp;--&nbsp;steps required to set up, test, roll out, and manage submission integration
 
*[[Submission Integration: Implementation]]&nbsp;--&nbsp;steps required to set up, test, roll out, and manage submission integration
 
*[[Submission Integration: Current Status]]&nbsp;--&nbsp;current status of Dryad's integrated journals
 
*[[Submission Integration: Current Status]]&nbsp;--&nbsp;current status of Dryad's integrated journals
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*[http://wiki.datadryad.org/Journal_instructions Journal instructions]&nbsp;-- elements of journal data policies, including data citation guidelines, and illustrative examples
  
 
== Further resources ==
 
== Further resources ==
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*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]
 
*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]]
 
*Format specifications for automated email notices to Dryad: [[Journal Metadata]]
*Sample text for [[/wg/dryad/images/e/e8/Email_to_authors_INTEGRATED_JOURNALS.doc|email to authors]] inviting them to deposit data in Dryad
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*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: [[/wg/dryad/images/c/c6/DryadIntegrationOverview.pdf|Integration Overview Slides (PDF)]].
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*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]
 
*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]
*[http://wiki.datadryad.org/WG:Journal_Integration_in_process Journal Integration in process]
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*Facilitating data publishing through journal integration: [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.
+
Please [mailto:director@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 07:51, 15 January 2016

What is submission integration with Dryad?

Integration with Dryad allows journals to facilitate data archiving by setting up automatic communications between journals and Dryad. Journal integration with Dryad is available at no cost for any journal that wishes to implement low-burden data archiving and enhance their published articles with links to data.

We invite journals to integrate their manuscript processing with Dryad for the benefit of their authors, regardless of their membership status in the Dryad organization.

Advantages of integration include:

  • streamlining the authors’ data deposit process
  • permanently linking the published article with its securely archived data
  • enhancing visibility of the article via linking from the data package
  • allowing authors to deposit complex and varied data types in robust re-usable formats
  • ensuring that data files are discoverable, indexed, and exposed to both web and bibliographic search engines
  • permitting embargoes to delay release of data, in accordance with journal policy
  • enable editorial oversight of data and/or peer review of data, concurrent with manuscript review

Editors and publishers interested in implementing integration may review this documentation and contact Dryad or fill out the Pre-Integration Questionnaire to begin the integration process.

How it works

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

Below is the typical process:

  1. Authors submit their manuscripts to the journal for consideration.
  2. Journal provides information about manuscripts to Dryad through automated notices from the manuscript processing system, which creates a provisional Dryad record for the data.
  3. Journal invites authors to archive data in Dryad, providing them a custom submission link that brings the author to the provisional record.
  4. Authors upload their files to Dryad using the submission link supplied by the journal; no redundant information need be entered and the article details are correct. The submission is assigned a Digital Object Identifier (DOI), which is sent to both the author and the journal.
  5. Dryad curators process and approve the data files and register the DOI.
  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 the data package back to the journal article. Dryad can also provide links to data in other repositories, including sequences in GenBank and phylogenetic trees in TreeBASE.

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

Available options and customizations

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

These are some of the critical questions for integrating journals:

  • Is data archiving voluntary or required?
  • Does the journal want to have (secure) access to the data during manuscript review?
  • Should the data be accessible in Dryad before the manuscript is submitted?
  • Should authors be able to set a one-year embargo for their data?
  • Should editors be able to set custom-length data embargoes (in special cases)?
  • At what point in the article publication process should the data be made available on the Dryad website?
  • Will the journal, publisher, or society sponsor Dryad's Data Publishing Charges on behalf of their authors?

Dryad supports multiple ways of receiving article or manuscript metadata from publishers. The simplest method involves reading email notifications, but we are also implementing a REST API for those desiring greater control over the data deposition process.

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

Documentation

Further resources

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