Difference between revisions of "Submission System"

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'''Status: being completed by Nescent. Enhancements may be completed by @mire.'''
 
  
A new submission system is being developed that will better integrate with journals.
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== Overview ==
  
See also the list of [[Use Cases]] and the [[Partner Submission Integration]].
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Dryad's submission system allows users to quickly and easily submit data packages. Key features include:
  
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#[[Submission_Integration:_Overview|Integration with journals]] -- allowing authors to automatically fill the Dryad forms with information from the journal's description of an article, and automatically notifying journal editors when a Dryad submission is completed.
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#Minimal description requirements -- Dryad minimizes the amount of typing/clicking required by submitters. Descriptions are automatically propagated from the article description to descriptions for individual data files. Reasonable defaults are set for the various choices available.
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#Integration with partner repositories -- allowing submitters to use Dryad information as a starting point for submitting content to another repository.
  
== Workflow for a New Article ==
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See also the journal-oriented [[Submission Integration]] page.
  
# Journal accepts the author's publication.
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== Instructions ==
# Journal mails Dryad with metadata.
 
# Journal mails author acceptance letter, which contains a link to the Dryad submission for that publication. If the primary corresponding author of the article is not the primary manager of the data set, the article author may forward the email to the data set author.
 
## Author follows the link.
 
## Author logs in to Dryad (or creates an account). ([[Media:SubmissionMockupLogin.png]])
 
## Author is presented with a publication page that allows "Edit Publication Details" and "Add Dataset". ([[Media:SubmissionMockupPubSummary.png]])
 
## Author may expand metadata for the publication. ([[Media:SubmissionMockupJournalPub.png]])
 
## Author uploads data, providing additional metadata for each data set. ([[Media:SubmissionMockupDataset.png]])
 
## Author may provide IDs of data sets in other repositories.
 
## Author may provide IDs of pre-existing data sets in Dryad.
 
## Author may choose to place data sets under embargo. (Default embargo period lasts until 1 year from the '''publication''' date.
 
## Author chooses to "Publish Datasets". ([[Media:SubmissionMockupPubSummary.png]])
 
# Dryad mails handle of '''publication''' record to journal editor. (At least one dataset must be present.)
 
# Journal editors may include the Dryad handle in the article.
 
# Journal sends the table of contents (including DOI list) for each issue to Dryad, so complete metadata can be extracted and the embargo period can officially start.
 
#* This may be the same information that is sent to Crossref and/or PubMedCentral.
 
  
== Workflow for an Article in a non-partner Journal ==
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An overview of the Dryad submission process can be seen in the [http://www.youtube.com/watch?v=RP33cl8tL28 Dryad submission video].
  
# Author logs in to Dryad (or creates an account).
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For a journal-oriented view of the process, see [[Submission Integration]].
# Author chooses "Deposit Data for a New Publication".
 
# Author is presented with an "Add Publication" page. This page looks similar to the "Edit Publication Details" page from the partner journal process, but all fields may be edited (and are initially blank). ([[Media:SubmissionMockupCreateNewPublication.png]])
 
# Author is presented with a publication page that allows "Edit Publication Details" and "Add Dataset".
 
# Author may edit/expand metadata for the publication.
 
# Author uploads data, providing additional metadata for each data set.
 
# Author may provide IDs of data sets in other repositories.
 
# Author may provide IDs of pre-existing data sets in Dryad.
 
# Author may choose to place data sets under embargo. (Default embargo period lasts until 1 year from the '''publication''' date.
 
# Author chooses to "Publish Datasets".
 
  
== Points to remember ==
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== Technical Documentation ==
  
* Dorothea has a great post about [http://cavlec.yarinareth.net/archives/2007/11/02/less-cognitive-load-faster-deposit/ making the repository submission process easier].
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Technical documents are available on several topics:
* Note the comments from [[WG:Team_Meetings#Nov._17|Jane's metadata class]]
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* [[Submission System Technology]]
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* [[Submission System Workflow]]
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* [[Journal Metadata Processing]]
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* [[BagIt_Handshaking|Integration with TreeBASE]]
  
== Notes for The American Naturalist ==
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== Design history ==
  
* Contacts: Michael Whitlock (Dryad Representative), Mark McPeek (editor-in-chief), Trish Morse (managing editor)
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Mockups of submission features:
* They use Editorial Manager, which can send automated email messages with particular merge fields embedded.
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* [[Submission System Mockups]]
* They do not track keywords in Editorial Manager. They are retrievable from the meta kewords tag on the web pages, though.
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* [[Login-Register Mockup]]
* Once the main submission system is set up, they would like to email all authors for articles from the past 5 years, and encourage them to submit data as well.
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* [[TreeBASE Submission Mockups]]
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* [[Repository Handshaking Mockup]]
  
=== Email procecssing ===
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Back-end submission features:
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* [[Submission System Updates Phase 3]]
  
Email processing is currently a somewhat manual process. It will become more automatic as the steps are refined.
 
 
Email processing steps:
 
# Select all messages in Mac Mail
 
# File/Save As...
 
# Move saved file into submission/journalEmail/temp
 
# cd /Users/dryad/submission/journalEmail/americanNaturalist/
 
# Remove the last generation of files, so they don't have the new contents appended:
 
rm *.xml
 
# Run the following command, replacing "myMailFile" with the name of the actual saved file:
 
perl -pe 'open STDOUT, ">out".++$n if /From\: /' <myMailFile >out
 
6. Run the mail file parser. Be careful when copying this command! It is easy to accidentally select the rest of the commands on the page.
 
java -cp /Users/dryad/tomcat6/webapps/StandAloneSubmit/WEB-INF/classes:/Users/dryad/tomcat6/webapps/StandAloneSubmit/WEB-INF/lib/log4j-1.2.13.jar submit.util.ParseEmail
 
7. Remove the temporary "out" files.
 
rm out*
 
8. Copy the parsed files into the ready directory. (Eventually, the submission system should just look in the email directory for these.)
 
cp *.xml /Users/dryad/submission/inSubmissionSystem/
 
9. Sync the files to the production server.
 
cp *.xml /Users/dryad/repo-production/submission/inSubmissionSystem/
 
 
A cron job copies these to the production server, with logs in /var/log/dryad-submission.log on eryops.
 
 
=== Acceptance letter URLs ===
 
 
The acceptance URL is of the form:
 
http://datadryad.org/submit?journalID=amNat&manu=xxxx
 
 
It is then redirected to the submission aspect:
 
http://datadryad.org/repo/dryadsubmit/jsubmit?journalID=amNat&manu=xxxx
 
 
After login, the aspect redirects to the login page of the submission system.
 
 
== Notes for Evolution ==
 
 
* Contacts: Mark Rausher (editor-in-chief), Jennifer Mahar (managing editor)
 
* They use ScholarOne's Manuscript Central.
 
* The publication process has several stages. We would most likely want to hook into the "online accept" stage, where the publication has been accepted, but is not yet in final form.
 
** Jennifer will see what she can send us, possibly a version of the email that goes to the publishing group, but hopefully with abstract and keywords added
 
* A DOI is available for the "online early" stage, but it is not clear whether this is the final DOI, or whether it is shared with the print version of the article.
 
* The term they use for bibliographic metadata is "core data".
 
* Links from the journal's site to Dryad: these cannot be implemented until high-level approval is given.
 
* Evolution publishes several types of papers -- which of these types should go to Dryad?
 
 
== Notes for Molecular Ecology ==
 
 
* Contacts: Tim Vines (managing editor)
 
* Tim has written a document on the [[Media:VinesManuscriptCentralSetup.pdf‎|Manuscript Central template for Dryad metadata]].
 
* Status: metadata transfer is working.
 
* Their abbreviation will be "molecol".
 
* They will add some random digits to the normal manuscript number for security purposes.
 
 
== Notes for Ecological Society of America ==
 
 
* Contacts: David Baldwin (managing editor), Anne Marie Whelan (Publications Coordinator)
 
* Want to start working on submission system ASAP.
 
* They use a submission system called Ejournal Press, and they contract with Allen Press to run it for them.
 
* We should write to David Baldwin to discuss integration of the submission process and they will convey our questions, etc. to the appropriate people at Allen Press.
 
* They already encourage submission to the ESA archives.
 
* They want to make sure the metadata standards follow what their Publications Committee recommends.
 
 
== Fleshing out metadata with publication information ==
 
 
CrossRef has published a [http://oxford.crossref.org/labs/best_practice/rss/rss_best_practice_recommendations.html draft recommendation] for journals to make their tables of contents machine-readable using RSS. If this is accepted by the community, it will greatly ease the process of obtaining complete metadata about articles that have been published.
 
 
== For Future Development ==
 
 
* We want the submission system to be implemented as a DSpace module, but not necessarily tied in to the existing submission system (because of its complexity).
 
* It is ok for end-users to use one system, and when they are done the item is kicked over to the existing workflow system for evaluation by curators.
 
 
* We seem to have some overlap with the Vireo submission system from TDL. Should we build on top of it??
 
 
[[Category:Work Packages]]
 
 
[[Category:Journals]]
 
[[Category:Journals]]
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[[Category:Help]]
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[[Category:Features]]

Latest revision as of 11:21, 22 June 2015

Overview

Dryad's submission system allows users to quickly and easily submit data packages. Key features include:

  1. Integration with journals -- allowing authors to automatically fill the Dryad forms with information from the journal's description of an article, and automatically notifying journal editors when a Dryad submission is completed.
  2. Minimal description requirements -- Dryad minimizes the amount of typing/clicking required by submitters. Descriptions are automatically propagated from the article description to descriptions for individual data files. Reasonable defaults are set for the various choices available.
  3. Integration with partner repositories -- allowing submitters to use Dryad information as a starting point for submitting content to another repository.

See also the journal-oriented Submission Integration page.

Instructions

An overview of the Dryad submission process can be seen in the Dryad submission video.

For a journal-oriented view of the process, see Submission Integration.

Technical Documentation

Technical documents are available on several topics:

Design history

Mockups of submission features:

Back-end submission features: