Submission System

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Status: initial work completed by Nescent. Enhancements are being evaluated by @mire.

See also the list of Use Cases and the Partner Submission Integration.


Workflow for a New Article

  1. Journal accepts the author's publication.
  2. Journal mails Dryad with metadata.
  3. 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.
    1. Author follows the link, which has the form: http://datadryad.org/submit?journalID=zzzz&manu=xxxx
    2. The link redirects to the DSpace aspect that handles submission: http://datadryad.org/repo/dryadsubmit/jsubmit?journalID=zzzz&manu=xxxx
    3. Author logs in to Dryad (or creates an account). (Media:SubmissionMockupLogin.png)
    4. Author is presented with a publication page that allows "Edit Publication Details" and "Add Dataset". (Media:SubmissionMockupPubSummary.png)
    5. Author may expand metadata for the publication. (Media:SubmissionMockupJournalPub.png)
    6. Author uploads data, providing additional metadata for each data set. (Media:SubmissionMockupDataset.png). The author may also include a "README" file with additional documentation (see a Dryad record with a README file).
    7. Author may provide IDs of data sets in other repositories.
    8. Author may provide IDs of pre-existing data sets in Dryad.
    9. Author may choose to place data sets under embargo. (Default embargo period lasts until 1 year from the publication date.
    10. Author chooses to "Publish Datasets". (Media:SubmissionMockupPubSummary.png)
  4. Dryad mails handle of publication record to journal editor. (At least one dataset must be present.)
  5. Journal editors may include the Dryad handle in the article.
  6. 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

  1. Author logs in to Dryad (or creates an account).
  2. Author chooses "Deposit Data for a New Publication".
  3. 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)
  4. Author is presented with a publication page that allows "Edit Publication Details" and "Add Dataset".
  5. Author may edit/expand metadata for the publication.
  6. Author uploads data, providing additional metadata for each data set.
  7. Author may provide IDs of data sets in other repositories.
  8. Author may provide IDs of pre-existing data sets in Dryad.
  9. Author may choose to place data sets under embargo. (Default embargo period lasts until 1 year from the publication date.
  10. Author chooses to "Publish Datasets".

Points to remember

Email Parsing System

  1. Email sent to a short perl script (journalEmailGateway.pl), which forwards the contents of the message to a web service.
  2. The web service (journal-submit) parses the contents of the email.
    • Parsing can be different for each journal, though most journals use the Manuscript Central template created by Tim Vines.
    • The parsed content is stored as an XML file in submission/journalMetadata.
  3. When an author follows a link (or enters an equivalent journalID and manuscript number into the submission web form), the submission system will import the relevant XML file to pre-populate metadata for the new submission.

Notes for The American Naturalist

  • Contacts: Michael Whitlock (Dryad Representative), Mark McPeek (editor-in-chief), Trish Morse (managing editor)
  • They use Editorial Manager, which can send automated email messages with particular merge fields embedded.
  • They do not track keywords in Editorial Manager. They are retrievable from the meta kewords tag on the web pages, though.
  • 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.

Testing timeline

  • Dryad first received metadata records on 2008-9-24.
  • URL processing went live on 2009-5-16.
  • Authors received Dryad links in acceptance letters starting 2009-8-26.

See American Naturalist Integration Issues.

Email procecssing

Email processing is currently a somewhat manual process. It will become more automatic as the steps are refined.

Email processing steps:

  1. Select all messages in Mac Mail
  2. File/Save As...
  3. Move saved file to the development server, into /Users/dryad/submission/journalEmail/temp
  4. On the development server, run /Users/dryad/bin/process-amnat.sh

A cron job copies the final files to the production server, with logs in /var/log/dryad-submission.log.


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 and Dryad Representative)
  • Tim has written a document on the Manuscript Central template for Dryad metadata.
  • Status: metadata transfer is working.
  • Their abbreviation will be "MolEcol".
  • Molecular Ecology Resources will use the abbreviation "MolEcolRes".
  • They will add some random digits to the normal manuscript number for security purposes.

Timeline:

  • URL processing went live on 2009-10-26.

Notes for Systematic Biology

  • Contacts: Rod Page (Dryad representative, past EIC), Debbie Ciszek (Managing Editor)
  • They already collect some types of data in Manuscript Central. The current plan is to expand this, so that all data is collected in Manuscript Central, and submitted directly to Dryad with little author involvement.

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 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.