terraref / data-paper Goto Github PK

Review instructions for authors and define scope of paper

I suspect from this API call https://terraref.ncsa.illinois.edu/bety/api/v1/search?cultivar=~PI_
that these were already replaced by removing underscore
Need to confirm that none of these have associated traits
Then remove records

• take inventory of contents
• remove material, metadata etc that is currently in dryad data pub and remove from this
• update list of tasks for data paper and categorize by importance and urgency

• add user stories
• links to documentation
• specific applications

• Scott: terraref-dryad.docx
• Steve K: Should reference BAP w/ Breton 2016 "A genomic resource for the development, improvement, and exploitation of sorghum for bioenergy"
• Noah: terraref/data-publication#3

• implement all revisions
• list authors identified
• compile
• submit

• sensor descriptions
• Trait data
• docs.terraref.org

• max create a catalog / manifest
• david to update text

• Seasons: 4&6
• Data Products:
  • Las plot clip
  • RGB plot clip
  • Thermal plot clip (season 6 only)
• Changes to sample:
  • all climate variables should be trimmed to 4 significant digits 123.4 or 0.01234)
  • remove gene_markers table
  • add data products (I only see RGB)

if it would help you avoid moving data around, you can run your scripts against the filesystem at workbench.terraref.org

TODO

• Chris add code to data-publication repo
• David review databases
• David document and upload to dryad submission

Feedback from @jdemieville-ua:

• General Information - dimension mismatch
  • Scannable area greater than 200 m x 20 m
  • Actual scannable was 22.135m on E/W and closer to 206m on N/S (Lower limit of 3.8m and upper limit around 209.3m if my memory is correct)
• Data Types/Sensor Data - Which sensors are counted in the 5? There were from my count 2 laser scanners, 2 RGB cameras, 1 thermal camera, 1 PS2 camera, 1 multispectral (Crop Circle), 2 hyperspectral scanners, 1 carbon dioxide sensor, 1 weather sensor, 4 light sensors (NDVI/PRI), 1 spectrometer (VNIR-range), and 1 PAR sensor installed in Season 6. It is also more accurate to say >4000m^2 area and <=1mm^2 resolution, as it may otherwise lead people to think we tried to get resolutions to match across sensors.
• Sensor Data/Field Scanner Sensors -
  • Stereo RGB - correct model
    • GT3300 -> Allied Vision Prosilica GT3300C
  • Laser Scanner - correct spelling
    • Frauhofer -> Fraunhofer
  • Thermal - correct model
    • SC 615 -> A615
  • PSII - correct model; technical specifications
    • Lemnatec PS II -> LemnaTec PS2 Camera
      • Only documentation available for camera calls it ‘PS2 Camera’
    • Can find no information in LemnaTec manual supporting the technical specifications listed
  • Environmental - correct model
    • Thies ClimaSensor -> Thies Clima 4.9200.00.000
  • VNIR Spectrometer - correct model, specifications
    • Spectral Evolution PSR+ -> Ocean Optics STS-VIS-L-50-400-SMA
    • 350-1000nm -> 350-800nm
  • PAR Sensor - correct model
    • Quantum SQ-300 -> Apogee Instruments SQ-214-SS
      • Additional Sensors; only models checked – did not review technical specifications
  • NDVI - change model
    • Skye Instruments SKR 1860D/A
  • PRI - change model
    • Skye Instruments SKR 1860ND/A
  • Crop Circle - change model
    • Holland Scientific Crop Circle ACS-430
  • SWIR Spectrometer
    • Where did this come from? No SWIR spectrometer was installed for S4/S6
  • CO2 - change model
    • Vaisala CARBOCAP Carbon Dioxide Probe GMP343

• research and summarize github README files
• research and summarize github issues and conversations therein
  • start w/ qaqc tag
  • review issues as you go
• write summary of what has been done
• meet with Max to review his work

• Review and summarize existing notes and todo lists
• Review contents of current data paper repository
• Create new manageable steps to migrate content and create figures for data paper

e.g. UAV data, old folders that need to be reprocessed

• outline data paper
  • Introduction
  • Methods
  • Data Use
  • Limits of data
  • Future releases
  • define key figures and tables
• use template and / or migrate outline from template to bookdown framework
• delete unused content from repository

As defined in outline: https://github.com/terraref/data-paper/blob/develop/outline.md

• Example for each dataset
  • Images for sensors
  • time series + p-values for traits
  • time series for weather variables
  • wavelength x time for spectrometer
• Overall data processing pipeline
• Examples for technical validation
  • masks
  • shade
  • tiles

Also describe late season drought experiment

related to genophenoenvo/terraref-datasets#85

Known errors in current genomics data; group at DDPSC is re-generating these and will update in CyVerse

Assign distinct DOI to these?