TERRA-REF Documentation
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Primary version
Primary version
  • Introduction
  • Scientific Objectives
  • Experimental Design
    • The Maricopa Agricultural Center (MAC)
    • Controlled Environment Phenotyping
    • Genomics
  • Data
    • How to Access Data
    • Data Products
      • Environmental conditions
      • Phenotype Data
      • Genomics data
      • Fluorescence intensity imaging
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Meteorological data
      • Point Cloud Data
      • Controlled Environment phenotype data
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
  • Protocols
    • Field Scanner
    • Sensor Calibration
    • Hyperspectral Data
    • Controlled Environment Protocols
    • Manual Field Data Protocols
    • Phenotractor Protocols
    • UAV Protocols
    • Genomic Protocols
  • Technical Documentation
    • Software
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Data Product Levels
    • Directory Structure
    • Data Transfer
    • Data Processing Pipeline
    • Time Series Data in Geostreams
    • Data Backup
    • Systems Configuration
  • Code of Conduct
  • Appendix
    • Glossary
    • Accessing BETYdb with GIS Software
  • References
  • Archived Documentation
    • Developer Manual
      • Submitting data to Clowder
      • Submitting data to BETYdb
      • Submitting Data to CoGe
      • Developing Clowder Extractors
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  • Databases
  • Clowder (sensor data and computation management with web user interface)
  • Globus Connect (large data transfer)
  • BETYdb (phenotype data)
  • Algorithms
  • Extractors
  • Plant CV
  • CoGe
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  1. Technical Documentation

Software

PreviousTechnical DocumentationNextData Standards

Last updated 5 years ago

TERRA-REF uses a suite of databases and software components to automate the analysis of sensor data to produce plant and plot level traits / phenotypes, store and provide access to data..

Databases

Clowder (sensor data and computation management with web user interface)

Clowder is the primary system used to organize, annotate, and process raw data generated by the phenotyping platforms as well as information about sensors. Use Clowder to explore the raw TERRA-REF data, perform exploratory analysis, and develop custom extractors. For more information, see Using Clowder.

Globus Connect (large data transfer)

BETYdb (phenotype data)

BETYdb is a database and web interface to the trait / phenotype data and agronomic metadata. This is where you can find plant and plot level trait data as well as plot locations and other information associated with agronomic experimental design. Use BETYdb to access derived trait and agronomic data. For more information, see Using BETYdb.

Algorithms

Extractors

Plant CV

CoGe

Raw data is transferred to the primary TERRA-REF compute pipeline using Globus Online. Globus also provides access to TERRA REF files, but this is not a primary portal and metadata in Clowder may be required to locate and interpret these files. Use Globus Online when you want to transfer data from the TERRA-REF system for local analysis by accessing the . For more information, see Using Globus.

Each step in the pipeline is performed by an algorithm. These are maintained in the TERRA REF GitHub organization in repositories with names that begin in extractors-* such as .

is an imaging processing package specific for plants that is built upon open-source software platforms , , and . Plant CV is used for trait identification, the output is stored in both Clowder and BETYdb.

is a platform for performing Comparative Genomics research. It provides an open-ended network of interconnected tools to manage, analyze, and visualize next-gen data. CoGe contains genomic information and sequence data from the TERRA REF project.

Terraref endpoint
github.com/terraref/extractors-hyperspectral
Plant CV
OpenCV
NumPy
MatPlotLib
CoGe