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2012-01-12 conference call

Agenda

BIEN_db_proposed_agenda_20120112.docx

Brad's to dos

BIEN_db_meeting_20120112.docx

Mapping tool

  • A "nice to have", and would greatly aid Aaron in mapping new (plot) data sources
  • But would be a big time sink (Mark; agreed by all)
  • Out of scope for this year; might be good to seek separate funding to develop this tool
  • Caveat: unless Aaron can identify some relatively "ready to use" tool to assist mapping (CLIO? modify VegBranch?)
  • Web interface
  • Postpone for now decision about platform, re-use of VegBank interface, who does it and when. After we have finalized database schema will discuss again.

Mapping and import procedure

  • Specimens:
    1. sourceDb→DwC_extract→(VegX)→VegBIEN
    2. sourceDb→DwC_extract→VegBIEN
    3. sourceDb→DwC_extract→DwC_BIEN→VegBIEN
    4. sourceDb→DwC_extract→DwC_BIEN→VegX→VegBIEN
      • Currently Aaron does #1, using VegX as path only (doesn't actually convert to XML
      • Should consider using different approach, either #3 or #4
      • Advantages of this approach is that the only arrow that would need to be customized for different data source is from DwC_extract→DwC_BIEN. Because DwC is simple, this task would be simple.
      • DwC_extract is provided by data provider
      • All remaining arrows (DwC_BIEN→VegX→VegBIEN) would need to be done only ONCE and never changed again.
      • Therefore we need to specify a the particular version of DwC to be used by BIEN
      • Brad will do this, and get back to Aaron
  • Plots
    1. sourceDb→VegX→VegBIEN
    2. plotDB→plot_extract→VegX→VegBIEN
      • The arrow from VegX→VegBIEN should be completed asap, and should be comprehensive, so can be used for all data sources without modification. This will require completion of : (a) revision of VegX schema (especially, to accommodate stems within individuals) and (b) VegBIEN (nearly complete, as per Bob's suggestions)

Aaron's to dos

  1. re-load SALVIAS with stems data
  2. Update statistics/lists of user-defined fields in use in VegX and VegBIEN
  3. Convert user-defined VegX fields to first-class fields
  4. Convert user-defined VegBIEN fields to first-class fields
  5. get access to raw CTFS data
  6. map NYBG data
  7. NYBG validations
  8. map CTFS data
    • map the individual organisms data, not the aggregated extract
  • add traits table to VegBIEN
  • generic MOU template to request data (Mark)
  • DwC extension to VegX
  • use VegX's individualOrganismObservation/relatedItem to model stems
  • make website user-protected
  • researchers OK w/ phpMyAdmin-style interface

added by Martha:

  • Decision: the schema mapping tool is out of scope. Could be funded separately. look into Clio
  • get raw data rather than flat file exports from RAINFOR
  • Brad to negotiate with Rick to try to get Aaron direct access to CTFS
  • Mapping processes
    • For specimen data: sourceDb -> DwC_extract -> DwC_BIEN(?) -> VegBIEN: switch to DwC-BIEN done
    • For plot data: sourceDb -> VegX ->?? -> VegBIEN
    • Avoids creating a dependency between DwC and VegX schemas
    • Does create a dependency between VegX and VegBIEN schemas
  • Hold off deciding about the web interface