Difference between revisions of "TreeBASE Submission Integration"

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  '''Status:''' Initial implementation is complete, but it will continue to be enhanced.
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== Overview ==
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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.
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Alternately, authors who initially submit content to TreeBASE may create a link from a Dryad data package to the relevant item in TreeBASE.
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== Instructions ==
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=== Initial submission to TreeBASE ===
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Authors may choose to deposit their data with TreeBASE first, and link the submission to a Dryad deposit.
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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.
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[[Image:1.png]]
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== Overview  ==
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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.
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[[Image:2.png]]
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=== (Disabled) Initial submission to Dryad ===
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{{StatusBox|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.}}
  
Authors who submit content to TreeBASE or Dryad will be have the option to make their content appear in both systems.
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The submission is initially deposited with Dryad. Data files are then forwarded from Dryad to TreeBASE.
  
TreeBASE content will be searchable through Dryad, even if the author has not explicitly included the content in a Dryad data package.
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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.
  
== Workflow ==
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[[Image:3.png]]
  
[todo: user description and pictures here]
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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.
  
== Process for completing a submission within TreeBASE ==
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[[Image:4.png]]
  
=== Minimum Requirements ===
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The author will receive two email messages:
* nexus file
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# A confirmation of the Dryad submission, including the DOI that Dryad has assigned to the submission.
** at least one tree OR at least one matrix
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# 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.
** if there is a tree and a matrix, the taxon labels must match up.
 
** must be "understood" by Mesquite
 
* citation
 
* analysis info linking matrices and trees
 
  
=== Detailed Process ===
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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.
  
* create account
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'''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.
* login
 
* create new submission
 
* type title
 
** the submission gets a PURL at this point
 
** the PURL can have a code added for reviewer access
 
* fill in citation
 
** minimum: year, title, journal name (or book/section title)
 
** journal names auto-suggest as you type
 
* add authors
 
** minimum: at least one author (with first name and last name)
 
** must always search for an existing author first, even if you know they're not in the system
 
** allows reordering or deleting authors while you're in the process
 
* upload file(s)
 
** minimum: must be nexus, as described above
 
* (optional) add notes
 
** this is a textarea, with a reasonable character limit (not enough for a readme file)
 
* (optional) edit details for matrices
 
* (optional) edit row segment template
 
** minimum: row ID, start index, end index
 
* (optional) provide more details for trees
 
* (optional) taxa
 
** match all named taxa against ubio or ncbi
 
** although the cleanup is optional, the TB editor may reject it if it's not cleaned up
 
* analysis
 
** minimum: create an analysis with at least one step. Typically, this will be a matrix that is processed to create one or more trees.
 
** minimum: otu labels must match in the analysis steps
 
* when initial submission complete, user clicks "change to ready state"
 
** this triggers the curator to look at it
 
** user can leave items as "in progress" as long as they want -- this is a "poor man's embargo" system
 
  
 
== Technical Documentation ==
 
== Technical Documentation ==
  
This integration will be based on the following technologies:
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More detail on the TreeBASE/BagIt handshaking can be found on the Dryad [[BagIt Handshaking]] page.
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This integration is based on the following technologies:
  
 
*[https://wiki.ucop.edu/display/Curation/BagIt BagIt] -- A lightweight format for packaging digital content and ensuring that it is transferred intact.
 
*[https://wiki.ucop.edu/display/Curation/BagIt BagIt] -- A lightweight format for packaging digital content and ensuring that it is transferred intact.
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We are evaluating the [http://purl.org/net/sword/ 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.
 
We are evaluating the [http://purl.org/net/sword/ 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.
  
 
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== Design History ==
More detail on the TreeBASE/BagIt handshaking can be found on the Dryad [http://code.google.com/p/dryad/wiki/BagItHandshaking technical documentation wiki]
 
  
  
See also: [[TreeBASE OAI Provider]]
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For information on design decisions, look at the [https://wiki.ucop.edu/display/Curation/BagIt BagIt] and [http://www.openarchives.org/pmh/ OAI-PMH] pages listed in the Technical documentation and at the [[TreeBASE OAI Provider]] page on this wiki.  We also looked at [http://www.jisc.ac.uk/whatwedo/programmes/mrd/rdmi/admiral.aspx ADMIRAL: A data management infrastructure for research across the life sciences]
  
 
[[Category:Other Repositories]]
 
[[Category:Other Repositories]]
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[[Category: Features]]
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[[Category:Help]]
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[[Category:Handshaking]]

Latest revision as of 10:51, 16 August 2016

Overview

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.

Instructions

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.


1.png


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.


2.png

(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.

3.png

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.

4.png

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