Difference between revisions of "TreeBASE Submission Integration"

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(Relevant Text from the Grant Proposal)
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== Relevant Text from the Grant Proposal ==
 
== Relevant Text from the Grant Proposal ==
  
* "\[handshaking\] so that, where required by the journal or requested by the author, data will simultaneously be deposited in Dryad and... TreeBASE."
+
* "[handshaking] so that, where required by the journal or requested by the author, data will simultaneously be deposited in Dryad and... TreeBASE."
 
* "Dryad will collect any metadata required by the target database that has not already been captured, submit the pertinent data to the target database using a non-interactive programmatic gateway, and obtain the submission status, accession numbers, or possible error messages from the target database."
 
* "Dryad will collect any metadata required by the target database that has not already been captured, submit the pertinent data to the target database using a non-interactive programmatic gateway, and obtain the submission status, accession numbers, or possible error messages from the target database."
 
* "For TreeBASE, we will design and implement a robust, web-service based submission Application Programming Interface (API). An extensive redesign of TreeBASE by the CIPRES project (www.phylo.org) is scheduled for release in 2007. However, it currently lacks a submission API. The software to be added will include the automated data validation steps that are part of the new TreeBASE submission process (e.g. validating the NEXUS format, matching terminal taxa against the uBio NameBank). When TreeBASE rejects a submission, the depositor will be notified, advised how to correct the problem, and asked to resubmit. "
 
* "For TreeBASE, we will design and implement a robust, web-service based submission Application Programming Interface (API). An extensive redesign of TreeBASE by the CIPRES project (www.phylo.org) is scheduled for release in 2007. However, it currently lacks a submission API. The software to be added will include the automated data validation steps that are part of the new TreeBASE submission process (e.g. validating the NEXUS format, matching terminal taxa against the uBio NameBank). When TreeBASE rejects a submission, the depositor will be notified, advised how to correct the problem, and asked to resubmit. "

Revision as of 11:33, 27 August 2009

Status: Nescent and Yale will begin work on this after the TreeBASE OAI Provider is complete.

Basic process:

  1. User submits to Dryad (and completes the submission).
  2. User is presented with a button "Also submit this content to TreeBASE"
  3. When the button is pressed, all relevant Dryad data/metadata is forwarded to TreeBASE (publication becomes a TreeBASE study, each tree & matrix becomes TreeBASE data).
  4. Items are in the TreeBASE submission system, waiting for the user to finish. The user can login to TreeBASE at any time and complete the submission, adding additional information as necessary. (Or they may ignore it)
  5. When TreeBASE submission is complete, either (a) TreeBASE notifies Dryad, or (b) Dryad picks up the submission in its next OAI-PMH harvest.
  6. Dryad matches the items to existing Dryad records, because the Dryad handles are present in the records that TreeBASE serves.

Whiteboard notes from the initial discussion, including integration with Dryad submissions:

TreebaseDryadCoordination.JPG

Relevant Text from the Grant Proposal

  • "[handshaking] so that, where required by the journal or requested by the author, data will simultaneously be deposited in Dryad and... TreeBASE."
  • "Dryad will collect any metadata required by the target database that has not already been captured, submit the pertinent data to the target database using a non-interactive programmatic gateway, and obtain the submission status, accession numbers, or possible error messages from the target database."
  • "For TreeBASE, we will design and implement a robust, web-service based submission Application Programming Interface (API). An extensive redesign of TreeBASE by the CIPRES project (www.phylo.org) is scheduled for release in 2007. However, it currently lacks a submission API. The software to be added will include the automated data validation steps that are part of the new TreeBASE submission process (e.g. validating the NEXUS format, matching terminal taxa against the uBio NameBank). When TreeBASE rejects a submission, the depositor will be notified, advised how to correct the problem, and asked to resubmit. "


See also: TreeBASE OAI Provider