Difference between revisions of "TreeBASE Submission Integration"

From Dryad wiki
Jump to: navigation, search
(Tasks)
(Process for submitting to TB)
Line 14: Line 14:
  
 
== Process for submitting to TB ==
 
== Process for submitting to TB ==
 +
 +
=== Minimum Requirements ===
 +
* citation
 +
* nexus file
 +
* analysis info linking matrices and trees
 +
 +
=== Detailed Process ===
  
 
* create account
 
* create account
Line 20: Line 27:
 
* type title
 
* type title
 
** the submission gets a PURL at this point
 
** the submission gets a PURL at this point
** the PURL can have a code added for reviewer access  
+
** the PURL can have a code added for reviewer access
 
* fill in citation
 
* fill in citation
 
** minimum: year, title, journal name (or book/section title)
 
** minimum: year, title, journal name (or book/section title)
Line 39: Line 46:
 
** match all named taxa against ubio or ncbi
 
** 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
 
** although the cleanup is optional, the TB editor may reject it if it's not cleaned up
* analysis  
+
* 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: 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
 
** minimum: otu labels must match in the analysis steps

Revision as of 07:12, 11 March 2010

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

NOTE: More details are available in the general Handshaking pages.

Workflow

Whiteboard notes from the initial discussion, including integration with Dryad submissions.
  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 as a SWORD package (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 Dryad picks up the submission in its next OAI-PMH harvest (from the TreeBASE OAI Provider).
  6. Dryad matches the items to existing Dryad records. Typically the matching will rely on Dryad handles being present in the records that TreeBASE serves via OAI, but matching may also rely on publication DOI, titles, or other metadata.

Process for submitting to TB

Minimum Requirements

  • citation
  • nexus file
  • analysis info linking matrices and trees

Detailed Process

  • create account
  • 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

Open Questions

  1. Can Dryad records be transferred immediately, or must they be approved by a Dryad curator first? If records are transferred before curator approval, when is the permanent ID assigned?
  2. Is it possible to carry over authentication? (single sign-on) Can/should Dryad track user account info on other systems? (or will everyone move to DataONE authentication?)
  3. Does the user have to press a button to submit to TreeBASE, or could it just be automatic? If we could link the user accounts, the submission could just show us when the user logs into TreeBASE.
  4. Should TreeBASE have a "pull" method, where users logged in to TreeBASE can import content with a Dryad ID?


Random Notes

  • TB does not make content available until the associated article is published
  • (new) TB only has one identifier, which is used all the way through the process
  • TB has thousands of in-progress submissions, which are waiting for the publication to be accepted.
  • Dryad often knows that an article has been accepted, and should tell TB about this
  • TB may have an embargo process, which Dryad should use for embargoed items

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