Old:Genomic Resources Notes Technology

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Status: See also: https://trello.com/c/GdcmikC2

Molecular Ecology Resources prints "summary" articles for all of the PCR primers submitted in a month. Authors of the individual primers may submit data packages to Dryad for them.


The goal of technology is to allow the authors of the primers to submit data packages to Dryad as they would for any normal article. The primary difference is that several data packages would be associated with the same summary article. A sample summary article is available at http://dx.doi.org/10.1111/j.1755-0998.2011.03109.x


Metadata Submission Emails

Molecular Ecology Resources will send emails for each data package, using the format described in Journal Metadata Processing Technology. The format used is based on Manuscript Central (EmailParserForManuscriptCentral.java), and GR Note submissions require additional metadata fields:

  • Article Type
  • MS Citation Title
  • MS Citation Author

Submissions for individual primer articles will still reference a unique manuscript number, so this identifier can still be used for submission uniqueness.

Sample metadata format:

Article Status: submitted
Article Type: GR Note    [or Regular for everything else]
MS Reference Number: ##DOCUMENT_ID##
MS Title: ##DOCUMENT_TITLE##     [the title used for the data package]
MS Citation Title: Genomic Resources Notes XXXX    [the XXXX would be updated to e.g. '1 April 2013 – 31 May 2013' in the confirmation email]
MS Authors: ##DOCUMENT_AUTHORS##     [these people would be the authors of the individual GR Note]
MS Citation Authors: Genome Resources Development Consortium et al.    [for 'Regular' Article Types this would be the same as 'MS Authors' ]

Submission process workflow

From the author/submitter's perspective, the submission process for a "GR Note" article is identical to a "Regular" article. The metadata is fetched by the Journal and the Manuscript ID, which still uniquely identify the pre-populated metadata.

However, since there are additoinal fields (MS Citation Title and MS Citation Authors), the submission process populates the DSpace Item objects differently:

  1. Add articleType, citationTitle, citationAuthors fields to PublicationBean (PublicationBean.java)
  2. Add mapping of citationTitle to dryad.citationTitle (dspace.cfg:submit.journal.metadata)
  3. Upon submission of data for a GR Note (SelectPublicationStep.java),
    • MS Title and MS Citation Title are formatted into dc.title. See citation sample
    • MS Citation Title is stored in a new metadata field, dryad.citationTitle
    • MS Citation Authors is ignored
    • MS Authors is stored in dc.contributor.author as usual
    • dc.identifier.citation will not be filled automatically. It will be filled by curators when the article is published.

Citation Sample:

When using this data, please cite the original article:

Genome Resources Development Consortium et al. (2013)
Genomic Resources Notes accepted 1 April 2013 – 31 May
2013. Molecular Ecology Resources 13(3): 903-913.

Additionally, please cite the Dryad data package:

MS Authors (2013) Data From: "MS Title" in Genomic
Resources Notes accepted 1 April 2013 – 31 May 2013.
Dryad Digital Repository. doi:10.5061/dryad.1nn7v


Requires a metadata field dryad.citationTitle to be created. The changes to dspace.cfg will store the value of MS Citation Title there.


Features Required

  • On the Dryad item page, we need to show "other data packages associated with this article" (lower priority)

Open Questions

  1. The editors would like to attach the PDF of each note to the data package. They will ensure authors know that the text will be released under CC0. How should we receive the PDFs?
    • Send them via email? This is the most straightforward extension of our submission system, and would likely tie in to design for the SWORD deposit mechanism
    • Have journal editors login to dryad and submit the PDFs directly? Should editors have direct access to add content to submissions?