Insert experimental design for 2016 Sorghum trials at MAC into TERRAREF BETYdb

[dlebauer]

Detailed Description

The Experimental design for Sorghum trials is defined in this google spreadsheet

Next steps

1. Define intended plot layouts and plant locations on the gantry reference system (meters offset from [0,0]. We need:
   • plot and alley dimensions
   • row spacing
   • locations of the corner of the first plot and first plant in that plot
     • we can start with the experimental design (as opposed to what we can later observe as the actual locations) and update the layout as necessary
     • if we have information that may not be accurate that is okay - we can update it later. Best if we have an estimate of the scale of uncertainty (e.g. within X cm)? For plot boundaries a few cm should be sufficiently precise.
     • we can compare and update the information with observed positions of the plants and outputs of the precision planter
2. later we can convert the plot layouts into geospatial data. This requires lat/lon coordinates for [0,0]
3. Import the genotypes information into the TERRAREF/BETYdb cultivars table

• Genotype information is stored in the "Source", "Common Name", and "Pedigree fields" of the 'Treatments'
• Identify the unique identifier / 'primary key' for these. Pedigree information can be later imported to BMS, and the primary key can link from BETYdb to BMS.

4. Import traits from Treatments table (Which traits are useful?)
   • BETYdb isn't currently set up to ingest categorical traits, this feature is requested in Enable variable to be categorical PecanProject/bety#409 and can be implemented if there is need
   • BMS does store categorical traits.
   • Which categorical variables can be converted to numeric values with date and location of observation?
     • for example, It would be preferable to store these as numeric values if possible. For example, instead of 'maturity group' we could store the phenological observations as boolean (0/1) This could be combined with date of planting or emergence to compute the number of days to any particular phenological stage and then the cutoffs could be defined (and altered if desired).
   • Where, when, and under what conditions was height measured?
5. import information from Experiments worksheet on google drive into experiments table in BETYdb
   • Create 'experiments' table (Add 'experiments' table to provide grouping and temporal context to sites PecanProject/bety#410)

@dlebauer - please touch base with Scott about this.

[dlebauer]

remaining issues:

• link cultivars to trait records Upload UAV NDVI data to terraref.org/bety #201 (comment)
• associate plots with experiments

Experiments

Season 1:

relationships are first two columns of https://docs.google.com/spreadsheets/d/1iHmSyFeCO7np_lxYyvdiXQQcAwBJpIKpeAOyMXFd-OY/edit#gid=901711246

• for each unique expt name in the speadsheet create an experiment record with the name "Season 1 --expt--"
  • experiment duration is planting date May 2016 to harvest in July 2016 (look in managements for exact dates; choose latest)
• add all of the associated sites where name like 'UA MAC Season 1 Plot [col B]%

For season 2:

• add a experiment named "Season 2 Stay-green RILs F10"
  • experiment duration is Aug 2016 to harvest in Dec 2016 see managements for exact dates (choose latest).
• add all sites where name like 'MAC Season 2%'

Cultivars

• run update statements in Upload UAV NDVI data to terraref.org/bety #201 (comment)
• for future, create cultivars_sites table + trigger to autopopulate as defined in Add cultivars_sites table PecanProject/bety#475