TreeBASE Submission Integration

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Revision as of 10:00, 19 April 2011 by Kc140 (talk | contribs) (Technical Documentation)

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Status: Initial implementation is complete, but it will continue to be enhanced.


Authors who submit content to TreeBASE or Dryad will be have the option to make their content appear in both systems.

TreeBASE content will be searchable through Dryad, even if the author has not explicitly included the content in a Dryad data package.


[todo: user description and pictures here]

Process for completing a submission within TreeBASE

Minimum Requirements

  • nexus file
    • at least one tree OR at least one matrix
    • 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

  • 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

Technical Documentation

This integration will be 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.

More detail on the TreeBASE/BagIt handshaking can be found on the Dryad technical documentation wiki

See also: TreeBASE OAI Provider