Database Interop Hackathon/Pre-Meeting

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The core developers of NeXML, CDAO, and PhyloWS met two weeks prior to the hackathon to better prepare the participating emerging standards for actual application at the hackathon.

Goals & Targets


  • Choose a very narrow limited set of goals, and include time to
    • evaluate carefully what we have done
    • extrapolate and plan for the big meeting when we have 20 people to keep busy
  • Need to discuss how to accommodate all the projects using php.

Target ideas:

  • Implement services that would allow Mesquite to query and retrieve character data and trees from TreeBASE and from MorphBank.
  • Agreeing on how to implement semantic annotation of metadata types of the providers.
  • More fleshing out of PhyloWS specs.

Information to gather in advance:

  • Implementation details of the providers: which languages/libraries they use, what metadata they want to expose.

Notes from meeting

Thursday, Feb 19

Participants arrive.

Fri, Feb 20

  • 9-10am: Priorities, use-cases, documentation needs
  • 10-11.30am: Objectives, goals, and assessments (with Jonathon Cummings)
  • 12-1pm BBL seminar at NESCent by Arlin Stoltzfus & Rutger Vos
  • 1-3pm
  • Agenda and outline for conference call
  • Remote participation tools set up
  • 3-4pm: Teleconference with hackathon participants
  • 4-6pm: Continuing earlier work & wrap-up for the day
    • Information gathering form for data types for I/O and formats
    • PhyloWS: Review of current spec against SRU (with Ryan Scherle).

Sat, Feb 21

  • 9.30am-12.30pm
    • Expression of metadata and metadata semantics in NeXML
      • Representation of references
    • Re-using existing metadata vocabularies (such as DC)
  • 12.30-1.30pm Lunch
  • 1.30-5pm
    • Expression of metadata and metadata semantics in NeXML
      • Generalize the solution for representing references
      • Attaching GO terms to tree nodes
      • Linking OTUs to taxon identifiers and to specimen records
  • 5-6pm Dinner
  • 6-8pm

Sun, Feb 22

  • 9am-12pm
    • Contining expression of metadata
      • reworking reference using more precise format recommended for Dublin Core
      • oops, NESCent lost our changes from last night
      • re-wrote our section on representing EQ annotations on phenotypes
    • Wrapping up and follow-up to-do list
      • Survey (Arlin)
        • edit to add category for metadata types
        • edit to add questions about impementations (what is primary language for data processing, i.e., middleware in 3-tier scheme; what is the indexing methcanism for text searches; all custom code or uses toolbox or other code base)
        • send live survey to participants
      • solicit feedback on examples (Hilmar)
        • from TDWG colleagues on assigning specimens to collections
        • from Berkely Onto group on ??
        • from hackathon participants on whether examples are useful and relevant
      • refactor wiki
        • "implementations" relocate (Hilmar)
        • nexml (Rutger)
      • encourage participants to enter use cases on wiki -- ask Dave & Karla (Hilmar)
      • distribute CDAO information (Arlin)
  • 1:30 Brandon & Enrico departed
  • 1:30 Lunch
  • 2:30 to 4:30 pm
    • see "to do" list above
  • 4:30 Arlin departed


The pre-meeting takes place Friday - Sunday, Feb 20-22, 2009 at NESCent in Durham, North Carolina.


Participant Affiliation Email Standard
Brandon Chisham New Mexico State University CDAO
Hilmar Lapp NESCent PhyloWS
Enrico Pontelli New Mexico State University CDAO
Arlin Stoltzfus NIST, U. Maryland CDAO
Rutger Vos University of British Columbia NeXML, PhyloWS