2013-01-31 conference call¶

Martha's summary¶

*Martha's meeting notes*:

• Brad: Circulate a written description/definition of the confusing fields for Bob to sign off on and Aaron to respond to if there are cases that don’t fit. (sourceaccessioncode [accessioncode] shouldn’t be there; add databaseid and barcode fields; clarify other confusing fields)
• Brad to follow-up re Chile and Argentina data: see HVAA
• MN: Alert Barbara re GBIF status.
• MN: Ask Brian E to contact Peter Jorgensen about MO refresh.
• MN: Request email update on CTFS from Brian.

Upcoming¶

• next week, revise FIA cultivated flag WHERE clause

To do¶

Analytical DB¶

• regenerate analytical DB w/ original, matched name

Data validation¶

• Update validation status list
• TEAM: Brad will validate TEAM if haven't heard from Eric by next week
• CTFS
  • use aggregated CTFS data if can't use individuals (we just need species lat/long)
  • Martha will e-mail Brian to get update
• higher priority than geovalidation

Data refresh¶

• MO: Peter Jorgensen has requested a reexport of the Tropicos specimens
• GBIF: MOU has been signed by NCEAS

Mappings¶

• map accession # -> catalogNumber (they are synonyms)
  • note that catalogNumber may be duplicated if the same # is stamped on multiple specimens
  • accession # is usually unique within the database, but is not necessarily the database pkey
• add databaseID, which stores the database pkey
• add barcode
• remap datasources to new terms
• occurrenceID should be URN as described by *DwC*: urn:[datasource]:[databaseID] or urn:[datasource]:[institutionCode]:[collectionCode]:[barcode|catalogNumber]
  • use barcode instead of catalogNumber when both specified

VegBIEN¶

• remove all accessioncode fields from VegBIEN; we don't use them

Geovalidation¶

• make geovalidation pipeline a web service

VegCore¶

• clarifications of DwC terms
  • occurrenceID/databaseID/barcode/catalogNumber
  • datasource/institutionCode/ownerInstitutionCode
  • DwC driven by animal collections, so much less standardized than herbarium data

New data¶

• Herbario Virtual Austral Americano
  • "a fledgling virtual herbarium for southern South America [...] They use the Symbiota software out of ASU, which allows you to download the full result set in DwC or Symbiota format (use the cryptic icon to the upper right of the formatted results). If you check all collections and enter a country ("Argentina" or "Chile") you can get a full set of specimens for that country. Note that some of the participating herbaria are already in BIEN, so you may have to remove duplicates by checking against what we already have. Hopefully we can track down some new specimens." (e-mail from Brad on 2013-1-31)
• Instituto de Botanica Darwinion
  • "I could see no way to easily search of download all specimens. Also, none of the specimens I checked had coordinates, so I'm not sure if this portal will be of much use" (e-mail from Brad on 2013-1-31)
• SEINET
  • "This is a consortium of herbaria from the SW USA. I believe all are in GBIF, but it might be work checking, just in case." (e-mail from Brad on 2013-1-31)