TreeBASE Submission Integration

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Revision as of 09:51, 16 August 2016 by Ryan Scherle (talk | contribs) ((Disabled) Initial submission to Dryad)

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Authors who submit content to Dryad have the option to forward their Dryad submission to TreeBASE. This saves the author time by automating the submission of data to multiple repositories, and creates an explicit link between the entries in the two repositories for easier data reuse.

Alternately, authors who initially submit content to TreeBASE may create a link from a Dryad data package to the relevant item in TreeBASE.


Initial submission to TreeBASE

Authors may choose to deposit their data with TreeBASE first, and link the submission to a Dryad deposit.

After the TreeBASE submission has been completed, the author will login to Dryad and begin a Dryad submission. At the second stage of the Dryad submission process, the author will be asked to provide the appropriate data file(s). At this point, rather than uploading a new copy of the file(s), the author may enter an identification number for the data and the name of the repository in which the data has been submitted.


So, if the data has already been uploaded to TreeBASE, instead of uploading the data again, a submitter may just enter the TreeBASE identifier and select TreeBASE as the remote repository from the dropdown menu in the submission form. This will create a link between the Dryad data record and the data stored in the remote repository.


(Disabled) Initial submission to Dryad

Status: The workflow no longer supports initial submission to Dryad. This feature was disabled due to usability concerns. The documentation will remain here in case we decide to reinstate the feature.

The submission is initially deposited with Dryad. Data files are then forwarded from Dryad to TreeBASE.

At the second stage of the Dryad submission process, a submitter will see the option to "choose file" from their local machine. This will upload the data into Dryad. When this has happened, the submission form's page will change to indicate the file size of the uploaded data file.


If a file has been uploaded through the "choose file" interface, at the last stage in the submission process, the author will be given the option to upload the file that has been uploaded to Dryad to TreeBASE as well. Checking the checkbox and selecting TreeBASE from the repository dropdown will initiate the file's upload to TreeBASE.


The author will receive two email messages:

  1. A confirmation of the Dryad submission, including the DOI that Dryad has assigned to the submission.
  2. A notification that TreeBASE has received the forwarded data files. In this message, there will be a URL for accessing the submission within the TreeBASE system.

The author will need to follow the URL from the second message. After logging in to TreeBASE, the author will be able to complete the TreeBASE description of the data files, entering information that was not already part of the Dryad submission.

NOTE: If files are embargoed when they are deposited at Dryad, these embargo settings will not carry over to TreeBASE by default. The author must select appropriate embargo settings in each system.

Technical Documentation

More detail on the TreeBASE/BagIt handshaking can be found on the Dryad BagIt Handshaking page.

This integration is based on the following technologies:

  • BagIt -- A lightweight format for packaging digital content and ensuring that it is transferred intact.
  • OAI-PMH -- A protocol developed by the digital library community to allow harvesting of metadata from remote repositories.

We are evaluating the SWORD protocol to manage the transfer of BagIt packages, but we have not yet determined whether SWORD will be lightweight enough to justify its use.

Design History

For information on design decisions, look at the BagIt and OAI-PMH pages listed in the Technical documentation and at the TreeBASE OAI Provider page on this wiki. We also looked at ADMIRAL: A data management infrastructure for research across the life sciences