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